MALDI-TOF mass spectrometry: An emerging technology for microbial identification and diagnosis

Frontiers in Microbiology

Volumn 6, Issue AUG, 2015, Pages

  Singhal, Neelja ^a   Kumar, Manish ^a   Kanaujia, Pawan ^a   Virdi, Jugsharan S ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

Bacterial identification; Fungi; MALDI TOF MS; Peptide mass fingerprint; Proteomics, viruses

Indexed keywords

RNA 16S; RNA 18S;

ANTIBIOTIC RESISTANCE; ANTIVIRAL RESISTANCE; BIOLOGICAL WARFARE; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DOT HYBRIDIZATION; GENE SEQUENCE; GENOTYPING TECHNIQUE; INFECTION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROBIAL IDENTIFICATION; POLYMERASE CHAIN REACTION; REVIEW; SENSITIVITY ANALYSIS;

EID: 84940941884     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2015.00791     Document Type: Review

References (197)

1. Alam, S. I., Kumar, B., and Kamboj, D. V. (2012). Multiplex detection of protein toxins using MALDI-TOF-TOF tandem mass spectrometry: application in unambiguous toxin detection from bioaerosol. Anal. Chem. 84, 10500-10507. doi: 10.1021/ac3028678
2. Alanio, A., Beretti, J. L., Dauphin, B., Mellado, E., Quesne, G., Lacroix, C., et al. (2011). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fast and accurate identification of clinically relevant Aspergillus species. Clin. Microbiol. Infect. 17, 750-755. doi: 10.1111/j.1469-0691.2010.03323.x
3. Alastruey-Izquierdo, A., Cuesta, I., Walther, G., Cuenca-Estrella, M., and Rodriguez-Tudela, J. L. (2010). Antifungal susceptibility profile of human-pathogenic species of Lichtheimia. Antimicrob. Agents Chemother. 54, 3058-3060. doi: 10.1128/AAC.01270-09
4. Alatoom, A. A., Cazanave, C. J., Cunningham, S. A., Ihde, S. M., and Patel, R. (2012). Identification of non-diphtheriae Corynebacterium by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 50, 160-163. doi: 10.1128/JCM.05889-11
5. Alatoom, A. A., Cunningham, S. A., Ihde, S. M., Mandrekar, J., and Patel, R. (2011). Comparison of direct colony method versus extraction method for identification of Gram-Positive cocci by use of bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 49, 2868-2873. doi: 10.1128/JCM.00506-11
6. Alby, K., Gilligan, P. H., and Miller, M. B. (2013). Comparison of matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry platforms for the identification of gram-negative rods from patients with cystic fibrosis. J. Clin. Microbiol. 51, 3852-3854. doi: 10.1128/JCM.01618-13
7. Alispahic, M., Christensen, H., Hess, C., Razzazi-Fazeli, E., Bisgaard, M., and Hess, M. (2011). Identification of Gallibacterium species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evaluated by multilocus sequence analysis. Int. J. Med. Microbiol. 301, 513-522. doi: 10.1016/j.ijmm.2011.03.001
8. Alshawa, K., Beretti, J. L., Lacroix, C., Feuilhade, M., Dauphin, B., Quesne, G., et al. (2012). Identification of clinical dermatophyte and Neoscytalidium species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 50, 2277-2281. doi: 10.1128/JCM.06634-11
9. Alvarez-Buylla, A., Culebras, E., and Picazo, J. J. (2012). Identification of Acinetobacter species: is Bruker biotyper MALDI-TOF mass spectrometry a good alternative to molecular techniques? Infect. Genet. Evol. 12, 345-349. doi: 10.1016/j.meegid.2012.01.002
10. Amiri-Eliasi, B., and Fenselau, C. (2001). Characterization of protein biomarkers desorbed by MALDI from whole fungal cells. Anal. Chem. 73, 5228-5231. doi: 10.1021/ac010651t
11. Angelakis, E., Million, M., Henry, M., and Raoult, D. (2011). Rapid and accurate bacterial identification in probiotics and yoghurts by MALDI-TOF mass spectrometry. J. Food Sci. 76, M568-M571. doi: 10.1111/j.1750-3841.2011.02369.x
12. Ayyadurai, S., Flaudrops, C., Raoult, D., and Drancourt, M. (2010). Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. BMC Microbiol. 10:285. doi: 10.1186/1471-2180-10-285
13. Bader, O. (2013). MALDI-TOF-MS-based species identification and typing approaches in medical mycology. Proteomics 13, 788-799. doi: 10.1002/pmic.201200468
14. Baillie, S., Ireland, K., Warwick, S., Wareham, D., and Wilks, M. (2013). Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry: rapid identification of bacteria isolated from patients with cystic fibrosis. Br. J. Biomed. Sci. 70, 144-148.
15. Barreiro, J. R., Ferreira, C. R., Sanvido, G. B., Kostrzewa, M., Maier, T., Wegemann, B., et al. (2010). Identification of subclinical cow mastitis pathogens in milk by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Dairy Sci. 93, 5661-5667. doi: 10.3168/jds.2010-3614
16. Bayliss, J., Moser, R., Bowden, S., and McLean, C. A. (2010). Characterisation of single nucleotide polymorphisms in the genome of JC polyomavirus using MALDI TOF mass spectrometry. J. Virol. Methods 164, 63-67. doi: 10.1016/j.jviromet.2009.11.029
17. Benagli, C., Rossi, V., Dolina, M., Tonolla, M., and Petrini, O. (2011). Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of clinically relevant bacteria. PLoS ONE 6:e16424. doi: 10.1371/journal.pone.0016424
18. Berrazeg, M., Diene, S. M., Drissi, M., Kempf, M., Richet, H., Landraud, L., et al. (2013). Biotyping of multidrug-resistant Klebsiella pneumoniae clinical isolates from France and Algeria using MALDI-TOF MS. PLoS ONE 8:e61428. doi: 10.1371/journal.pone.0016428
19. Bizzini, A., Durussel, C., Bille, J., Greub, G., and Prod'hom, G. (2010). Performance of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of bacterial strains routinely isolated in a clinical microbiology laboratory. J. Clin. Microbiol. 48, 1549-1554. doi: 10.1128/JCM.01794-09
20. Bizzini, A., Jaton, K., Romo, D., Bille, J., Prod'hom, G., and Greub, G. (2011). Matrix-assisted laser desorption ionization-time of flight mass spectrometry as an alternative to 16S rRNA gene sequencing for identification of difficult-To-identify bacterial strains. J. Clin. Microbiol. 49, 693-696. doi: 10.1128/JCM.01463-10
21. Böhme, K., Fernández-No, I. C., Barros-Velázquez, J., Gallardo, J. M., Calo-Mata, P., and Cañas, B. (2010). Species differentiation of seafood spoilage and pathogenic gram-negative bacteria by MALDI-TOF mass fingerprinting. J. Proteome Res. 9, 3169-3183. doi: 10.1021/pr100047q
22. Böhme, K., Fernández-No, I. C., Barros-Velázquez, J., Gallardo, J. M., Cañas, B., and Calo-Mata, P. (2011). Rapid species identification of seafood spoilage and pathogenic Gram-positive bacteria by MALDI-TOF mass fingerprinting. Electrophoresis 32, 2951-2965. doi: 10.1002/elps.201100217
23. Böhme, K., Fernández-No, I. C., Barros-Velázquez, J., Gallardo, J. M., Cañas, B., and Calo-Mata, P. (2012). SpectraBank: an open access tool for rapid microbial identification by MALDI-TOF MS fingerprinting. Electrophoresis 33, 2138-2142. doi: 10.1002/elps.201200074
24. Burillo, A., Rodríguez-Sánchez, B., Ramiro, A., Cercenado, E., Rodríguez-Créixems, M., and Bouza, E. (2014). Gram-stain plus MALDI-TOF MS (Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry) for a rapid diagnosis of urinary tract infection. PLoS ONE 9:e86915. doi: 10.1371/journal.pone.0086915
25. Calderaro, A., Arcangeletti, M. C., Rodighiero, I., Buttrini, M., Gorrini, C., Motta, F., et al. (2014). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry applied to virus identification. Sci. Rep. 4, 6803. doi: 10.1038/srep06803
26. Carbonnelle, E., Beretti, J. L., Cottyn, S., Quesne, G., Berche, P., Nassif, X., et al. (2007). Rapid identification of Staphylococci isolated in clinical microbiology laboratories by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 45, 2156-2161. doi: 10.1128/JCM.02405-06
27. Carbonnelle, E., Grohs, P., Jacquier, H., Day, N., Tenza, S., Dewailly, A., et al. (2012). Robustness of two MALDI-TOF mass spectrometry systems for bacterial identification. J. Microbiol. Methods 89, 133-136. doi: 10.1016/j.mimet.2012.03.003
28. Cash, P. (2009). Proteomics in the study of the molecular taxonomy and epidemiology of bacterial pathogens. Electrophoresis 1, S133-S141. doi: 10.1002/elps.200900059
29. Cassagne, C., Pratlong, F., Jeddi, F., Benikhlef, R., Aoun, K., Normand, A. C., et al. (2014). Identification of Leishmania at the species level with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin. Microbiol. Infect. 20, 551-557. doi: 10.1111/1469-0691.12387
30. Chen, H. Y., and Chen, Y. C. (2005). Characterization of intact Penicillium spores by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 19, 3564-3568. doi: 10.1002/rcm.2229
31. Cherkaoui, A., Emonet, S., Fernandez, J., Schorderet, D., and Schrenzel, J. (2011). Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification of Beta-hemolytic streptococci. J. Clin. Microbiol. 49, 3004-3005. doi: 10.1128/JCM.00240-11
32. Cherkaoui, A., Hibbs, J., Emonet, S., Tangomo, M., Girard, M., Francois, P., et al. (2010). Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J. Clin. Microbiol. 48, 1169-1175. doi: 10.1128/JCM.01881-09
33. Chou, T. C., Hsu, W., Wang, C. H., Chen, Y. J., and Fang, J. M. (2011). Rapid and specific influenza virus detection by functionalized magnetic nanoparticles and mass spectrometry. J. Nanobiotechnol. 9, 52. doi: 10.1186/1477-3155-9-52
34. Christner, M., Rohde, H., Wolters, M., Sobottka, I., Wegscheider, K., and Aepfelbacher, M. (2010). Rapid identification of bacteria from positive blood culture bottles by use of matrix-assisted laser desorption-ionization time of flight mass spectrometry fingerprinting. J. Clin. Microbiol. 48, 1584-1591. doi: 10.1128/JCM.01831-09
35. Couderc, C., Nappez, C., and Drancourt, M. (2012). Comparing inactivation protocols of Yersinia organisms for identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 26, 710-714. doi: 10.1002/rcm.6152
36. Croxatto, A., Prod'hom, G., and Greub, G. (2012). Applications of MALDI-TOF mass spectrometry in clinical diagnostic microbiology. FEMS Microbiol. Rev. 36, 380-407. doi: 10.1111/j.1574-6976.2011.00298.x
37. Demarco, M. L., and Burnham, C. A. (2014). Diafiltration MALDI-TOF mass spectrometry method for culture-independent detection and identification of pathogens directly from urine specimens. Am. J. Clin. Pathol. 141, 204-212. doi: 10.1309/AJCPQYW3B6JLKILC
38. Dieckmann, R., Graeber, I., Kaesler, I., Szewzyk, U., and von Döhren, H. (2005). Rapid screening and dereplication of bacterial isolates from marine sponges of the sula ridge by intact-cell-MALDI-TOF mass spectrometry (ICM-MS). Appl. Microbiol. Biotechnol. 67, 539-548. doi: 10.1007/s00253-004-1812-2
39. Dieckmann, R., and Malorny, B. (2011). Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 77, 4136-4146. doi: 10.1128/AEM.02418-10
40. Dong, H., Kemptner, J., Marchetti-Deschmann, M., Kubicek, C. P., and Allmaier, G. (2009). Development of a MALDI two-layer volume sample preparation technique for analysis of colored conidia spores of Fusarium by MALDI linear TOF mass spectrometry. Anal. Bioanal. Chem. 395, 1373-1383. doi: 10.1007/s00216-009-3067-3
41. Donohue, M. J., Best, J. M., Smallwood, A. W., Kostich, M., Rodgers, M., and Shoemaker, J. A. (2007). Differentiation of Aeromonas isolated from drinking water distribution systems using matrix-assisted laser desorption/ionization-mass spectrometry. Anal. Chem. 79, 1939-1946. doi: 10.1021/ac0611420
42. Donohue, M. J., Smallwood, A. W., Pfaller, S., Rodgers, M., and Shoemaker, J. A. (2006). The development of a matrix-assisted laser desorption/ionization mass spectrometry-based method for the protein fingerprinting and identification of Aeromonas species using whole cells. J. Microbiol. Methods 65, 380-389. doi: 10.1016/j.mimet.2005.08.005
43. Downard, K. M. (2013). Proteotyping for the rapid identification of influenza virus and other biopathogens. Chem. Soc. Rev. 42, 8584-8595. doi: 10.1039/c3cs60081e
44. Dubois, D., Leyssene, D., Chacornac, J. P., Kostrzewa, M., Schmit, P. O., Talon, R., et al. (2010). Identification of a variety of Staphylococcus species by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 48, 941-945. doi: 10.1128/JCM.00413-09
45. EI Khéchine, A., Couderc, C., Flaudrops, C., Raoult, D., and Drancourt, M. (2011). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of mycobacteria in routine clinical practice. PLoS ONE 6:e24720. doi: 10.1371/journal.pone.0024720
46. Eddabra, R., Prévost, G., and Scheftel, J. M. (2012). Rapid discrimination of environmental Vibrio by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Microbiol. Res. 167, 226-230. doi: 10.1016/j.micres.2011.09.002
47. Ekström, S., Onnerfjord, P., Nilsson, J., Bengtsson, M., Laurell, T., and Marko-Varga, G. (2000). Integrated microanalytical technology enabling rapid and automated protein identification. Anal. Chem. 72, 286-293. doi: 10.1021/ac990731l
48. Emonet, S., Shah, H. N., Cherkaoui, A., and Schrenzel, J. (2010). Application and use of various mass spectrometry methods in clinical microbiology. Clin. Microbiol. Infect. 16, 1604-1613. doi: 10.1111/j.1469-0691.2010.03368.x
49. Erhard, M., Hipler, U. C., Burmester, A., Brakhage, A. A., and Wöstemeyer, J. (2008). Identification of dermatophyte species causing onychomycosis and tinea pedis by MALDI-TOF mass spectrometry. Exp. Dermatol. 17, 356-361. doi: 10.1111/j.1600-0625.2007.00649.x
50. Espinal, P., Seifert, H., Dijkshoorn, L., Vila, J., and Roca, I. (2011). Rapid and accurate identification of genomic species from the Acinetobacter baumannii (Ab) group by MALDI-TOF MS. Clin. Microbiol. Infect. 18, 1097-1103. doi: 10.1111/j.1469-0691.2011.03696.x
51. Everley, R. A., Mott, T. M., Wyatt, S. A., Toney, D. M., and Croley, T. R. (2008). Liquid chromatography/mass spectrometry characterization of Escherichia coli and Shigella species. J. Am. Soc. Mass Spectrom. 19, 1621-1628. doi: 10.1016/j.jasms.2008.07.003
52. Fagerquist, C. K., Garbus, B. R., Miller, W. G., Williams, K. E., Yee, E., Bates, A. H., et al. (2010). Rapid identification of protein biomarkers of Escherichia coli O157:H7 by matrix-assisted laser desorption ionization-time-of-flight-time-of-flight mass spectrometry and top-down proteomics. Anal. Chem. 82, 2717-2725. doi: 10.1021/ac902455d
53. Feli, G., and Dellaglio, F. (2007). On the species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.). Int. J. Syst. Evol. Microbiol. 57, 2185-2187. doi: 10.1099/ijs.0.64931-0
54. Feltens, R., Görner, R., Kalkhof, S., Gröger-Arndt, H., and von Bergen, M. (2010). Discrimination of different species from the genus Drosophila by intact protein profiling using matrix-assisted laser desorption ionization mass spectrometry. BMC Evol. Biol. 10:95. doi: 10.1186/1471-2148-10-95
55. Fenselau, C., and Demirev, P. A. (2001). Characterization of intact microorganisms by MALDI mass spectrometry. Mass. Spectrom. Rev. 20, 157-171. doi: 10.1002/mas.10004
56. Fernandes, N. D., and Downard, K. M. (2014). Origins of the reassortant 2009 pandemic influenza virus through proteotyping with mass spectrometry. J. Mass Spectrom. 49, 93-102. doi: 10.1002/jms.3310
57. Fernández-No, I. C., Böhme, K., Gallardo, J. M., Barros-Velázquez, J., Cañas, B., and Calo-Mata, P. (2010). Differential characterization of biogenic amine-producing bacteria involved in food poisoning using MALDI-TOF mass fingerprinting. Electrophoresis 31, 1116-1127.
58. Ferreira, L., Sánchez-Juanes, F., García-Fraile, P., Rivas, R., Mateos, P. F., Martínez-Molina, E., et al. (2011). MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae. PLoS ONE 6:e20223. doi: 10.1371/journal.pone.0020223
59. Ferreira, L., Sánchez-Juanes, F., González-Avila, M., Cembrero-Fuciños, D., Herrero-Hernández, A., and González-Buitrago, J. M. (2010). Direct identification of urinary tract pathogens from urine samples by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 48, 2110-2115. doi: 10.1128/JCM.02215-09
60. Foster, A. G. (2013). Rapid Identification of microbes in positive blood cultures by use of the vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system. J. Clin. Microbiol. 51, 3717-3719. doi: 10.1128/JCM.01679-13
61. Friedrichs, C., Rodloff, A. C., Chhatwal, G. S., Schellenberger, W., and Eschrich, K. (2007). Rapid identification of Viridans Streptococci by mass spectrometric discrimination. J. Clin. Microbiol. 45, 2392-2397. doi: 10.1128/JCM.00556-07
62. Ganova-Raeva, L., Ramachandran, S., Honisch, C., Forbi, J. C., Zhai, X., and Khudyakov, Y. (2010). Robust hepatitis B virus genotyping by mass spectrometry. J. Clin. Microbiol. 48, 4161-4168. doi: 10.1128/JCM.00813-10
63. Gibb, S., and Strimmer, K. (2012). MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 28, 2270-2271. doi: 10.1093/bioinformatics/bts447
64. Griffin, P. M., Price, G. R., Schooneveldt, J. M., Schlebusch, S., Tilse, M. H., Urbanski, T., et al. (2012). Use of matrix-assisted laser desorption ionization-time of flight mass spectrometry to identify vancomycin-resistant enterococci and investigate the epidemiology of an outbreak. J. Clin. Microbiol. 50, 2918-2931. doi: 10.1128/JCM.01000-12
65. Guembe, M., Rodríguez-Sánchez, B., Ruiz, A., Martín-Rabadán, P., Rodríguez-Créixems, M., and Bouza, E. (2014). Can MALDI-TOF mass spectrometry be used with intravascular catheters? Enferm. Infecc. Microbiol. Clin. 32, 372-374. doi: 10.1016/j.eimc.2014.01.011
66. Haag, A., Taylor, M. S. N., Johnston, K. H., and Cole, R. B. (1998). Rapid identification and speciation of aemophilus bacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Mass Spectrom. 33, 750-756. doi: 10.1002/(SICI)1096-9888(199808)33:8<750::AID-JMS680>3.0.CO,2-1
67. Haigh, J. D., Green, I. M., Ball, D., Eydmann, M., Millar, M., and Wilks, M. (2013). Rapid identification of bacteria from bioMérieux BacT/ALERT blood culture bottles by MALDI-TOF MS. Br. J. Biomed. Sci. 70, 149-155.
68. Hart, P. J., Wey, E., McHugh, T. D., Balakrishnan, I., and Belgacem, O. (2015). A method for the detection of antibiotic resistance markers in clinical strains of Escherichia coli using MALDI mass spectrometry. J. Microbiol. Methods 111, 1-8. doi: 10.1016/j.mimet.2015.01.020
69. Hazen, T. H., Martinez, R. J., Chen, Y., Lafon, P. C., Garrett, N. M., Parsons, M. B., et al. (2009). Rapid identification of Vibrio parahaemolyticus by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 75, 6745-6756. doi: 10.1128/AEM.01171-09
70. He, Y., Chang, T. C., Li, H., Shi, G., and Tang, Y. W. (2011). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry and database for identification of Legionella species. Can. J. Microbiol. 57, 533-538. doi: 10.1139/w11-039
71. He, Y., Li, H., Lu, X., Stratton, C. W., and Tang, Y. W. (2010). Mass spectrometry biotyper system identifies enteric bacterial pathogens directly from colonies grown on selective stool culture media. J. Clin. Microbiol. 48, 3888-3892. doi: 10.1128/JCM.01290-10
72. Hettick, J. M., Green, B. J., Buskirk, A. D., Kashon, M. L., Slaven, J. E., Janotka, E., et al. (2008a). Discrimination of Penicillium isolates by matrix-assisted laser desorption/ionization time of- flight mass spectrometry fingerprinting. Rapid Commun. Mass Spectrom. 22, 2555-2560. doi: 10.1002/rcm.3649
73. Hettick, J. M., Green, B. J., Buskirk, A. D., Kashon, M. L., Slaven, J. E., Janotka, E., et al. (2008b). Discrimination of Aspergillus isolates at the species and strain level by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry fingerprinting. Anal. Biochem. 380, 276-281. doi: 10.1016/j.ab.2008.05.051
74. Hettick, J. M., Kashon, M. L., Simpson, J. P., Siegel, P. D., Mazurek, G. H., and Weissman, D. N. (2004). Proteomic profiling of intact mycobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal. Chem. 76, 5769-5776. doi: 10.1021/ac049410m
75. Hijazin, M., Alber, J., Lämmler, C., Weitzel, T., Hassan, A. A., Timke, M., et al. (2011). Identification of Trueperella (Arcanobacterium) bernardiae by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and by species-specific PCR. J. Med. Microbiol. 61, 457-459. doi: 10.1099/jmm.0.035774-0
76. Hooff, G. P., van Kampen, J. J., Meesters, R. J., van Belkum, A., Goessens, W. H., and Luider, T. M. (2012). Characterization of ß-lactamase enzyme activity in bacterial lysates using MALDI-mass spectrometry. J. Proteome Res. 11, 79-84. doi: 10.1021/pr200858r
77. Hoppenheit, A., Murugaiyan, J., Bauer, B., Steuber, S., Clausen, P.-H., and Roesler, U. (2013). Identification of Tsetse (Glossina spp.) using matrix-assisted laser desorption/ionisation time of flight mass spectrometry. PLoS Negl. Trop. Dis. 7:e2305. doi: 10.1371/journal.pntd.0002305
78. Horneffer, V., Forsmann, A., Strupat, K., Hillenkamp, F., and Kubitscheck, U. (2001). Localization of analyte molecules in MALDI preparations by confocal laser scanning microscopy. Anal. Chem. 73, 1016-1022. doi: 10.1021/ac000499f
79. Hoyos-Mallecot, Y., Cabrera-Alvargonzalez, J. J., Miranda-Casas, C., Rojo-Martín, M. D., Liebana-Martos, C., and Navarro-Marí, J. M. (2014). MALDI-TOF MS, a useful instrument for differentiating metallo-ß-lactamases in Enterobacteriaceae and Pseudomonas spp. Lett. Appl. Microbiol. 58, 325-329. doi: 10.1111/lam.12203
80. Hrabák, J., Walková, R., Studentová, V., Chudácková, E., and Bergerová, T. (2011). Carbapenemase activity detection by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 49, 3222-3227. doi: 10.1128/JCM.00984-11
81. Idelevich, E. A., Schüle, I., Grünastel, B., Wüllenweber, J., Peters, G., and Becker, K. (2014). Rapid identification of microorganisms from positive blood cultures by MALDI-TOF mass spectrometry subsequent to very short-term incubation on solid medium. Clin. Microbiol. Infect. 20, 1001-1006. doi: 10.1111/1469-0691.12640
82. Ilina, E. N., Borovskaya, A. D., Malakhova, M. M., Vereshchagin, V. A., Kubanova, A. A., Kruglov, A. N., et al. (2009). Direct bacterial profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for identification of pathogenic Neisseria. J. Mol. Diagn. 11, 75-86. doi: 10.2353/jmoldx.2009.080079
83. Ilina, E. N., Borovskaya, A. D., Serebryakova, M. V., Chelysheva, V. V., Momynaliev, K. T., Maier, T., et al. (2010). Application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the study of Helicobacter pylori. Rapid Commun. Mass Spectrom. 24, 328-334. doi: 10.1002/rcm.4394
84. Ilina, E. N., Malakhova, M. V., Generozov, E. V., Nikolaev, E. N., and Govorun, V. M. (2005). Matrix-assisted laser desorption ionization-time of flight (mass spectrometry) for hepatitis C virus genotyping. J. Clin. Microbiol. 43, 2810-2815. doi: 10.1128/JCM.43.6.2810-2815.2005
85. Jeong, Y. S., Choi, S., Chong, E., Kim, J. H., and Kim, S. J. (2014). Rapid detection of Bacillus spore aerosol particles by direct in situ analysis using MALDI-TOF mass spectrometry. Lett. Appl. Microbiol. 59, 177-178. doi: 10.1111/lam.12261
86. Jeong, Y. S., Lee, J., and Kim, S. J. (2013). Discrimination of Bacillus anthracis spores by direct in-situ analysis of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Bull Korean Chem. Soc. 34, 2635-2639. doi: 10.5012/bkcs.2013.34.9.2635
87. Johansson, A., Nagy, E., Sóki, J., and ESGAI (ESCMID Study Group on Anaerobic Infections). (2014). Detection of carbapenemase activities of Bacteroides fragilis strains with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Anaerobe 26, 49-52. doi: 10.1016/j.anaerobe.2014.01.006
88. Jungblut, P. R., and Hecker, M. (2004). Proteomics of microbial pathogens. Proteomics 4, 2829-2830. doi: 10.1002/pmic.200490063
89. Kemptner, J., Marchetti-Deschmann, M., Mach, R., Druzhinina, I. S., Kubicek, C. P., and Allmaier, G. (2009). Evaluation of matrix-assisted laser desorption/ionization (MALDI) preparation techniques for surface characterization of intact Fusarium spores by MALDI linear time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 23, 877-884. doi: 10.1002/rcm.3949
90. Kiehntopf, M., Melcher, F., Hänel, I., Eladawy, H., and Tomaso, H. (2011). Differentiation of Campylobacter species by surface-enhanced laser desorption/ionization-time-of-flight mass spectrometry. Foodborne Pathog. Dis. 8, 875-885. doi: 10.1089/fpd.2010.0775
91. Kilian, M., Poulsen, K., Blomqvist, T., Håvarstein, L. S., Bek-Thomsen, M., Tettelin, H., et al. (2008). Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS ONE 3:e2683. doi: 10.1371/journal.pone.0002683
92. Kliem, M., and Sauer, S. (2012). The essence on mass spectrometry based microbial diagnostics. Curr. Opin. Microbiol. 15, 397-402. doi: 10.1016/j.mib.2012.02.006
93. Köhling, H. L., Bittner, A., Müller, K. D., Buer, J., Becker, M., Rübben, H., et al. (2012). Direct identification of bacteria in urine samples by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and relevance of defensins as interfering factors. J. Med. Microbiol. 61, 339-344. doi: 10.1099/jmm.0.032284-0
94. Kostrzewa, M., Sparbier, K., Maier, T., and Schubert, S. (2013). MALDI-TOF MS: an upcoming tool for rapid detection of antibiotic resistance in microorganisms. Proteomics Clin. Appl. 7, 767-778. doi: 10.1002/prca.201300042
95. Kuhnert, P., Bisgaard, M., Korczak, B. M., Schwendener, S., Christensen, H., and Frey, J. (2012). Identification of animal Pasteurellaceae by MALDI-TOF mass spectrometry. J. Microbiol. Methods 89, 1-7. doi: 10.1016/j.mimet.2012.02.001
96. Kull, S., Pauly, D., Störmann, B., Kirchner, S., Stämmler, M., Dorner, M. B., et al. (2010). Multiplex detection of microbial and plant toxins by immunoaffinity enrichment and matrix-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 82, 2916-2924. doi: 10.1021/ac902909r
97. Kumar, M. P., Vairamani, M., Raju, R. P., Lobo, C., Anbumani, N., Kumar, C. P., et al. (2004). Rapid discrimination between strains of beta haemolytic streptococci by intact cell mass spectrometry. Indian J. Med. Res. 119, 283-288.
98. La Scola, B., and Raoult, D. (2009). Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry. PLoS ONE 4:e8041. doi: 10.1371/journal.pone.0008041
99. Lamy, B., Kodjo, A., Laurent, F., and ColBVH Study Group. (2011). Identification of Aeromonas isolates by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Diagn. Microbiol. Infect. Dis. 71, 1-5. doi: 10.1016/j.diagmicrobio.2011.04.014
100. Lartigue, M. F., Héry-Arnaud, G., Haguenoer, E., Domelier, A. S., Schmit, P. O., van der Mee-Marquet, N., et al. (2009). Identification of Streptococcus agalactiae isolates from various phylogenetic lineages by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 47, 2284-2287. doi: 10.1128/JCM.00175-09
101. Lasch, P., Beyer, W., Nattermann, H., Stämmler, M., Siegbrecht, E., Grunow, R., et al. (2009). Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks. Appl. Environ. Microbiol. 75, 7229-7242. doi: 10.1128/AEM.00857-09
102. Lasch, P., Nattermann, H., Erhard, M., Stämmler, M., Grunow, R., Bannert, N., et al. (2008). MALDI-TOF mass spectrometry compatible inactivation method for highly pathogenic microbial cells and spores. Anal. Chem. 80, 2026-2034. doi: 10.1021/ac701822j
103. Lau, A. F., Drake, S. K., Calhoun, L. B., Henderson, C. M., and Zelazny, A. M. (2013). Development of a clinically comprehensive database and a simple procedure for identification of molds from solid media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 51, 828-834. doi: 10.1128/JCM.02852-12
104. Lavergne, R. A., Chauvin, P., Valentin, A., Fillaux, J., Roques-Malecaze, C., Arbnaud, S., et al. (2013). An extraction method of positive blood cultures for direct identification of Candida species by Vitek MS matrix-assisted laser desorption ionization time of flight mass spectrometry. Med. Mycol. 51, 652-656. doi: 10.3109/13693786.2012.762607
105. Lay, J. O. Jr. (2001). MALDI-TOF mass spectrometry of bacteria. Mass Spectrom. Rev. 20, 172-194. doi: 10.1002/mas.10003
106. Lefmann, M., Honisch, C., Böcker, S., Storm, N., von Wintzingerode, F., and Schlötelburg, C. (2004). Novel mass spectrometry-based tool for genotypic identification of mycobacteria. J. Clin. Microbiol. 42, 339-346. doi: 10.1128/JCM.42.1.339-346.2004
107. Li, T. Y., Liu, B. H., and Chen, Y. C. (2000). Characterization of Aspergillus spores by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 14, 2393-2400. doi: 10.1002/1097-0231(20001230)14:24<2393::AID-RCM178>3.0.CO,2-9
108. Lista, F., Reubsaet, F. A., De Santis, R., Parchen, R. R., de Jong, A. L., Kieboom, J., et al. (2011). Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS. BMC Microbiol. 11:267. doi: 10.1186/1471-2180-11-267
109. Luan, J., Yuan, J., Li, X., Jin, S., Yu, L., Liao, M., et al. (2009). Multiplex detection of 60 hepatitis B virus variants by maldi-tof mass spectrometry. Clin. Chem. 55, 1503-1509. doi: 10.1373/clinchem.2009.124859
110. Lundquist, M., Caspersen, M. B., Wikström, P., and Forsman, M. (2005). Discrimination of Francisella tularensis subspecies using surface enhanced laser desorption ionization mass spectrometry and multivariate data analysis. FEMS Microbiol. Lett. 243, 303-310. doi: 10.1016/j.femsle.2004.12.020
111. Luo, Y., Siu, G. K., Yeung, A. S., Chen, J. H., Ho, P. L., Leung, K. W., et al. (2015). Performance of the VITEK MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid bacterial identification in two diagnostic centers in China. J. Med. Microbiol. 64, 18-24. doi: 10.1099/jmm.0.080317-0
112. Mc Taggart, L. R., Lei, E., Richardson, S. E., Hoang, L., Fothergill, A., and Zhang, S. X. (2011). Rapid identification of Cryptococcus neoformans and Cryptococcus gattii by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 49, 3050-3053. doi: 10.1128/JCM.00651-11
113. Mellmann, A., Cloud, J., Maier, T., Keckevoet, U., Ramminger, I., Iwen, P., et al. (2008). 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. 46, 1946-1954. doi: 10.1128/JCM.00157-08
114. Mencacci, A., Monari, C., Leli, C., Merlini, L., De Carolis, E., Vella, A., et al. (2013). Typing of nosocomial outbreaks of Acinetobacter baumannii by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 51, 603-606. doi: 10.1128/JCM.01811-12
115. Munoz, R., López-López, A., Urdiain, M., Moore, E. R., and Rosselló-Móra, R. (2011). Evaluation of matrix-assisted laser desorption ionization-time of flight whole cell profiles for assessing the cultivable diversity of aerobic and moderately halophilic prokaryotes thriving in solar saltern sediments. Syst. Appl. Microbiol. 34, 69-75. doi: 10.1016/j.syapm.2010.11.012
116. Muroi, M., Shima, K., Nakagawa, Y., and Tanamoto, K. (2011). Application of matrix-assisted laser desorption ionization-time of flight mass spectrometry for discrimination of Escherichia strains possessing highly conserved ribosomal RNA gene sequences. Biol. Pharm. Bull. 34, 430-432. doi: 10.1248/bpb.34.430
117. Murray, P. R. (2012). What is new in clinical microbiology-microbial identification by MALDI-TOF mass spectrometry. J. Mol. Diagn. 14, 419-423. doi: 10.1016/j.jmoldx.2012.03.007
118. Nagy, E., Maier, T., Urban, E., Terhes, G., Kostrzewa, M., and ESCMID Study Group on Antimicrobial Resistance in Anaerobic Bacteria. (2009). Species identification of clinical isolates of Bacteroides by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry. Clin. Microbiol. Infect. 15, 796-802. doi: 10.1111/j.1469-0691.2009.02788.x
119. Nakano, S., Matsumura, Y., Kato, K., Yunoki, T., Hotta, G., Noguchi, T., et al. (2014). Differentiation of vanA-positive Enterococcus faecium from vanA-negative E. faecium by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Int. J. Antimicrob. Agents 44, 256-259. doi: 10.1016/j.ijantimicag.2014.05.006
120. Ndukum, J., Atlas, M., and Datta, S. (2011). pkDACLASS: open source software for analyzing MALDI-TOF data. Bioinformation 6, 45-47. doi: 10.6026/97320630006045
121. Nenoff, P., Erhard, M., Simon, J. C., Muylowa, G. K., Herrmann, J., Rataj, W., et al. (2013). MALDI-TOF mass spectrometry - a rapid method for the identification of dermatophyte species. Med. Mycol. 51, 17-24. doi: 10.3109/13693786.2012.685186
122. Nguyen, D. T., Van Hoorde, K., Cnockaert, M., De Brandt, E., Aerts, M., Binh Thanh, L., et al. (2013). A description of the lactic acid bacteria microbiota associated with the production of traditional fermented vegetables in Vietnam. Int. J. Food Microbiol. 163, 19-27. doi: 10.1016/j.ijfoodmicro.2013.01.024
123. Nicolaou, N., Xu, Y., and Goodacre, R. (2012). Detection and quantification of bacterial spoilage in milk and pork meat using MALDI-TOF-MS and multivariate analysis. Anal. Chem. 84, 5951-5958. doi: 10.1021/ac300582d
124. Nilsson, C. L. (1999). Fingerprinting of Helicobacter pylori strains by matrix assisted laser desorption/ionization mass spectrometric analysis. Rapid Commun. Mass Spectrom. 13, 1067-1071. doi: 10.1002/(SICI)1097-0231(19990615)13:11<1067::AID-RCM612>3.0.CO,2-N
125. Nørskov-Lauritsen, N., Bruun, B., Andersen, C., and Kilian, M. (2012). Identification of haemolytic Haemophilus species isolated from human clinical specimens and description of Haemophilus sputorum sp. nov. Int. J. Med. Microbiol. 302, 78-83. doi: 10.1016/j.ijmm.2012.01.001
126. O'Leary, A. M., Whyte, P., Madden, R. H., Cormican, M., Moore, J. E., Mc Namara, E., et al. (2011). Pulsed field gel electrophoresis typing of human and retail foodstuff Campylobacters: an irish perspective. Food Microbiol. 28, 426-433. doi: 10.1016/j.fm.2010.10.003
127. Pace, N. L. (1997). A molecular view of microbial diversity and the biosphere. Science 276, 734-740. doi: 10.1126/science.276.5313.734
128. Pan, Y. L., Chow, N. H., Chang, T. C., and Chang, H. C. (2011). Identification of lethal Aspergillus at early growth stages based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Diagn. Microbiol. Infect. Dis. 70, 344-354. doi: 10.1016/j.diagmicrobio.2011.03.007
129. Patel, R. (2015). MALDI-TOF MS for the diagnosis of infectious diseases. Clin. Chem. 61, 100-111. doi: 10.1373/clinchem.2014.221770
130. Peng, J., Yang, F., Xiong, Z., Guo, J., Du, J., Hu, Y., et al. (2013). Sensitive and rapid detection of viruses associated with hand foot and mouth disease using multiplexed MALDI-TOF analysis. J. Clin. Virol. 56, 170-174. doi: 10.1016/j.jcv.2012.10.020
131. Perera, M. R., Vanstone, V. A., and Jones, M. G. (2005). A novel approach to identify plant parasitic nematodes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 19, 1454-1460. doi: 10.1002/rcm.1943
132. Pfaller, M. A., Messer, S. A., Hollis, R. J., Jones, R. N., and SENTRY Participants Group. (2002). Antifungal activities of posaconazole, ravuconazole, and voriconazole compared to those of itraconazole and amphotericin B against 239 clinical isolates of Aspergillus spp. and other filamentous fungi: report from SENTRY Antimicrobial Surveillance Program, 2000. Antimicrob. Agents Chemother. 46, 1032-1037. doi: 10.1128/AAC.46.4.1032-1037.2002
133. Piao, J., Jiang, J., Xu, B., Wang, X., Guan, Y., Wu, W., et al. (2012). Simultaneous detection and identification of enteric viruses by PCR-mass assay. PLoS ONE 7:e42251. doi: 10.1371/journal.pone.0042251
134. Pierce, C. Y., Barr, J. R., Woolfitt, A. R., Moura, H., Shaw, E. I., Thompson, H. A., et al. (2007). Strain and phase identification of the U.S. category B agent Coxiella burnetii by matrix assisted laser desorption/ionization time-of-flight mass spectrometry and multivariate pattern recognition. Anal. Chim. Acta 583, 23-31. doi: 10.1016/j.aca.2006.09.065
135. Prod'hom, G., Bizzini, A., Durussel, C., Bille, J., and Greub, G. (2010). Matrix-assisted laser desorption ionization-time of flight mass spectrometry for direct bacterial identification from positive blood culture pellets. J. Clin. Microbiol. 48, 1481-1483. doi: 10.1128/JCM.01780-09
136. Pulcrano, G., Roscetto, E., Iula, V. D., Panellis, D., Rossano, F., and Catania, M. R. (2012). MALDI-TOF mass spectrometry and microsatellite markers to evaluate Candida parapsilosis transmission in neonatal intensive care units. Eur. J. Clin. Microbiol. Infect. Dis. 31, 2919-2928. doi: 10.1007/s10096-012-1642-6
137. Qian, J., Cutler, J. E., Cole, R. B., and Cai, Y. (2008). MALDI-TOF mass signatures for differentiation of yeast species, strain grouping and monitoring of morphogenesis markers. Anal. Bioanal. Chem. 392, 439-449. doi: 10.1007/s00216-008-2288-1
138. Quirino, A., Pulcrano, G., Rametti, L., Puccio, R., Marascio, N., Catania, M. R., et al. (2014). Typing of Ochrobactrum anthropi clinical isolates using automated repetitive extragenic palindromic-polymerase chain reaction DNA fingerprinting and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. BMC Microbiol. 14:74. doi: 10.1186/1471-2180-14-74
139. Raus, M., and Šebela, M. (2013). BIOSPEAN: a freeware tool for processing spectra from MALDI intact cell/spore mass spectrometry. J. Proteomics. Bioinform. 6, 282-287.
140. Rosselló, G. A., Rodríguez, M. P., de Lejarazu Leonardo, R. O., Domingo, A. O., and Pérez, M. A. (2014). New procedure for rapid identification of microorganisms causing urinary tract infection from urine samples by mass spectrometry (MALDI-TOF). Enferm. Infecc. Microbiol. Clin. 33, 89-94. doi: 10.1016/j.eimc.2014.02.022
141. Ruelle, V., EI Moualij, B., Zorzi, W., Ledent, P., and Pauw, E. D. (2004). Rapid identification of environmental bacterial strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 18, 2013-2019. doi: 10.1002/rcm.1584
142. Saffert, R. T., Cunningham, S. A., Ihde, S. M., Kristine, E., Monson, J., Patel, R., et al. (2011). Comparison of bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to BD phoenix automated microbiology system for identification of gram-negative bacilli. J. Clin. Microbiol. 49, 887-892. doi: 10.1128/JCM.01890-10
143. Saleeb, P. G., Drake, S. K., Murray, P. R., and Zelazny, A. M. (2011). Identification of mycobacteria in solid-culture media by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 49, 1790-1794. doi: 10.1128/JCM.02135-10
144. Samson, R. A., and Varga, J. (2009). What is a species in Aspergillus? Med. Mycol. 47, S13-S20. doi: 10.1080/13693780802354011
145. Santos, C., Paterson, R. R., Venâncio, A., and Lima, N. (2010). Filamentous fungal characterizations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Appl. Microbiol. 108, 375-385. doi: 10.1111/j.1365-2672.2009.04448.x
146. Schröd, W., Heydel, T., Schwartze, V. U., Hoffmann, K., Grosse-Herrenthey, A., Walther, G., et al. (2012). Direct analysis and identification of pathogenic Lichtheimia species by matrix-assisted laser desorption ionization-time of flight analyzer-mediated mass spectrometry. J. Clin. Microbiol. 50, 419-427. doi: 10.1128/JCM.01070-11
147. Schwahn, A. B., Wong, J. W., and Downard, K. M. (2009). Subtyping of the influenza virus by high resolution mass spectrometry. Anal. Chem. 81, 3500-3506. doi: 10.1021/ac900026f
148. Schwahn, A. B., Wong, J. W., and Downard, K. M. (2010). Typing of human and animal strains of influenza virus with conserved signature peptides of matrix M1 protein by high resolution mass spectrometry. J. Virol. Methods 165, 178-185. doi: 10.1016/j.jviromet.2010.01.015
149. Segawa, S., Sawai, S., Murata, S., Nishimura, M., Beppu, M., Sogawa, K., et al. (2014). Direct application of MALDI-TOF mass spectrometry to cerebrospinal fluid for rapid pathogen identification in a patient with bacterial meningitis. Clin. Chim. Acta. 435, 59-61. doi: 10.1016/j.cca.2014.04.024
150. Seibold, E., Maier, T., Kostrzewa, M., Zeman, E., and Splettstoesser, W. (2010). Identification of Francisella tularensis by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry: fast, reliable, robust, and cost-effective differentiation on species and subspecies levels. J. Clin. Microbiol. 48, 1061-1069. doi: 10.1128/JCM.01953-09
151. Sendid, B., Ducoroy, P., François, N., Lucchi, G., Spinali, S., Vagner, O., et al. (2013). Evaluation of MALDI-TOF mass spectrometry for the identification of medically-important yeasts in the clinical laboratories of Dijon and Lille hospitals. Med. Mycol. 51, 25-32. doi: 10.3109/13693786.2012.693631
152. Seng, P., Drancourt, M., Gouriet, F., La Scola, B., Fournier, P. E., Rolain, J. M., et al. (2009). Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.Clin. Infect. Dis. 49, 543-551. doi: 10.1086/600885
153. Seyfarth, F., Ziemer, M., Sayer, H. G., Burmester, A., Erhard, M., Welker, M., et al. (2008). The use of ITS DNA sequence analysis and MALDI-TOF mass spectrometry in diagnosing an infection with Fusarium proliferatum. Exp. Dermatol. 17, 965-971. doi: 10.1111/j.1600-0625.2008.00726.x
154. Shaw, E. I., Moura, H., Woolfitt, A. R., Ospina, M., Thompson, H. A., and Barr, J. R. (2004). Identification of biomarkers of whole Coxiella burnetii phase I by MALDI-TOF mass spectrometry. Anal. Chem. 76, 4017-4022. doi: 10.1021/ac030364k
155. Shitikov, E., Ilina, E., Chernousova, L., Borovskaya, A., Rukin, I., Afanas'ev, M., et al. (2012). Mass spectrometry based methods for the discrimination and typing of mycobacteria. Infect. Genet. Evol. 12, 838-845. doi: 10.1016/j.meegid.2011.12.013
156. Sjöholm, M. I., Dillner, J., and Carlson, J. (2008). Multiplex detection of human herpesviruses from archival specimens by using matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 46, 540-545. doi: 10.1128/JCM.01565-07
157. Spanu, T., Posteraro, B., Fiori, B., D'Inzeo, T., Campoli, S., Ruggeri, A., et al. (2012). Direct maldi-tof mass spectrometry assay of blood culture broths for rapid identification of Candida species causing bloodstream infections: an observational study in two large microbiology laboratories. J. Clin. Microbiol. 50, 176-179. doi: 10.1128/JCM.05742-11
158. Sparbier, K., Schubert, S., Weller, U., Boogen, C., and Kostrzewa, M. (2012a). Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based functional assay for rapid detection of resistance against ß-lactam antibiotics. J. Clin. Microbiol. 50, 927-937. doi: 10.1128/JCM.05737-11
159. Sparbier, K., Weller, U., Boogen, C., and Kostrzewa, M. (2012b). Rapid detection of Salmonella sp. by means of a combination of selective enrichment broth and MALDI-TOF MS. Eur. J. Clin. Microbiol. Infect. Dis. 31, 767-773. doi: 10.1007/s10096-011-1373-0
160. Stackebrandt, E., and Goebel, B. M. (1994). A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44, 846-849. doi: 10.1099/00207713-44-4-846
161. Stephan, R., Cernela, N., Ziegler, D., Pflüger, V., Tonolla, M., Ravasi, D., et al. (2011). Rapid species specific identification and subtyping of Yersinia enterocolitica by MALDI-TOF mass spectrometry. J. Microbiol. Methods 87, 150-153. doi: 10.1016/j.mimet.2011.08.016
162. Stephan, R., Ziegler, D., Pflüger, V., Vogel, G., and Lehner, A. (2010). Rapid genus- and species-specific identification of Cronobacter spp. by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 48, 2846-2851. doi: 10.1128/JCM.00156-10
163. Stevenson, L. G., Drake, S. K., and Murray, P. R. (2010a). Rapid identification of bacteria in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 48, 444-447. doi: 10.1128/JCM.01541-09
164. Stevenson, L. G., Drake, S. K., Shea, Y. R., Zelazny, A. M., and Murray, P. R. (2010b). Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species. J. Clin. Microbiol. 48, 3482-3486. doi: 10.1128/JCM.00687-09
165. Strohalm, M., Hassman, M., Kosata, B., and Kodícek, M. (2008). mMass data miner: an open source alternative for mass spectrometric data analysis. Rapid Commun. Mass Spectrom. 22, 905-908. doi: 10.1002/rcm.3444
166. Tadros, M., and Petrich, A. (2013). Evaluation of MALDI-TOF mass spectrometry and Sepsityper KitTM for the direct identification of organisms from sterile body fluids in a Canadian pediatric hospital. Can. J. Infect. Dis. Med. Microbiol. 24, 191-194.
167. Theel, E. S., Hall, L., Mandrekar, J., and Wengenack, N. L. (2011). Dermatophyte identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 49, 4067-4071. doi: 10.1128/JCM.01280-11
168. Theel, E. S., Schmitt, B. H., Hall, L., Cunningham, S. A., Walchak, R. C., Patel, R., et al. (2012). Formic acid-based direct, on-plate testing of yeast and Corynebacterium species by Bruker Biotyper matrix-assisted laserdesorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 50, 3093-3095. doi: 10.1128/JCM.01045-12
169. Tiwari, V., and Tiwari, M. (2014). Quantitative proteomics to study carbapenem resistance in Acinetobacter baumannii. Front. Microbiol. 5:512. doi: 10.3389/fmicb.2014.00512
170. Torsvik, V. L., Øvreas, L., and Thingstad, T. F. (2002). Prokaryotic diversity - magnitude, dynamics, and controlling factors. Science 296, 1064-1066. doi: 10.1126/science.1071698
171. Uhlik, O., Strejcek, M., Junkova, P., Sanda, M., Hroudova, M., Vlcek, C., et al. (2011). Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil. Appl. Environ. Microbiol. 77, 6858-6866. doi: 10.1128/AEM.05465-11
172. Valentine, N., Wunschel, S., Wunschel, D., Petersen, C., and Wahl, K. (2005). Effect of culture conditions on microorganism identification by matrix-assisted laser desorption ionization mass spectrometry. Appl. Environ. Microbiol. 71, 58-64. doi: 10.1128/AEM.71.1.58-64.2005
173. van Baar, B. L. (2000). Characterisation of bacteria by matrix-assisted laser desorption/ionisation and electrospray mass spectrometry. FEMS Microbiol. Rev. 24, 193-219. doi: 10.1016/S0168-6445(99)00036-4
174. van Veen, S. Q., Claas, E. C., and Kuijper, E. J. (2010). High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J. Clin. Microbiol. 48, 900-907. doi: 10.1128/JCM.02071-09
175. Vandamme, P., Vancanneyt, M., van Belkum, A., Segers, P., Quint, W. G., Kersters, K., et al. (1996). Polyphasic analysis of strains of the genus Capnocytophaga and Centers for Disease Control group DF-3. Int. J. Syst. Bacteriol. 46, 782-791. doi: 10.1099/00207713-46-3-782
176. Verroken, A., Janssens, M., Berhin, C., Bogaerts, P., Huang, T. D., Wauters, G., et al. (2010). Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of Nocardia species. J. Clin. Microbiol. 48, 4015-4021. doi: 10.1128/JCM.01234-10
177. Vila, J., Juiz, P., Salas, C., Almela, M., de la Fuente, C. G., Zboromyrska, Y., et al. (2012). Identification of clinically relevant Corynebacterium spp., Arcanobacterium haemolyticum and Rhodococcus equi by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 50, 1745-1747. doi: 10.1128/JCM.05821-11
178. von Bergen, M., Eidner, A., Schmidt, F., Murugaiyan, J., Wirth, H., Binder, H., et al. (2009). Identification of harmless and pathogenic algae of the genus Prototheca by MALDI-MS. Proteomics Clin. Appl. 3, 774-784. doi: 10.1002/prca.200780138
179. Vranakis, I., Papadioti, A., Tselentis, Y., Psaroulaki, A., and Tsiotis, G. (2013). The contribution of proteomics towards deciphering the enigma of Coxiella burnetii. Proteomics Clin. Appl. 7, 193-204. doi: 10.1002/prca.201200096
180. Walker, J., Fox, A. J., Edwards-Jones, V., and Gordon, D. B. (2002). Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility. J. Microbiol. Methods 48, 117-126. doi: 10.1016/S0167-7012(01)00316-5
181. Wallet, F., Loãez, C., Decoene, C., and Courcol, R. (2011). Rapid identification of Cardiobacterium hominis by MALDI-TOF mass spectrometry during infective endocarditis. Jpn. J. Infect. Dis. 64, 327-329.
182. Wang, J., Chen, W. F., and Li, Q. X. (2012). Rapid identification and classification of Mycobacterium spp. using whole-cell protein barcodes with matrix assisted laser desorption ionization time of flight mass spectrometry in comparison with multigene phylogenetic analysis. Anal. Chim. Acta 716, 133-137. doi: 10.1016/j.aca.2011.12.016
183. Wang, L. J., Lu, X. X., Wu, W., Sui, W. J., and Zhang, G. (2014). Application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in the screening of vanA-positive Enterococcus faecium. Eur. J. Mass Spectrom. 20, 461-465. doi: 10.1255/ejms.1298
184. Wang, Y., Cui, S., and Li, F. (2008). Study on detection and identification of Salmonella species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Wei. Sheng. Yan. Jiu. 37, 685-689.
185. Wang, Z., Russon, L., Li, L., Roser, D. C., and Long, S. R. (1998). Investigation of spectral reproducibility in direct analysis of bacteria proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 12, 456-464. doi: 10.1002/(SICI)1097-0231(19980430)12:8<456::AID-RCM177>3.0.CO;2-U
186. Wasinger, V. C., Cordwell, S. J., Cerpa-Poljak, A., Yan, J. X., Gooley, A. A., Wilkins, M. R., et al. (1995). Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16, 1090-1094. doi: 10.1002/elps.11501601185
187. Welker, M. (2011). Proteomics for routine identification of microorganisms. Proteomics 11, 3143-3153. doi: 10.1002/pmic.201100049
188. Woese, C., Kandler, O., and Wheelis, M. L. (1990). Towards a natural system of organisms: proposals for the domains Achaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U.S.A. 87, 4576-4579. doi: 10.1073/pnas.87.12.4576
189. Wolters, M., Rohde, H., Maier, T., Belmar-Campos, C., Franke, G., Scherpe, S., et al. (2011). MALDI-TOF MS fingerprinting allows for discrimination of major methicillin-resistant Staphylococcus aureus lineages. Int. J. Med. Microbiol. 301, 64-68. doi: 10.1016/j.ijmm.2010.06.002
190. Wunschel, D. S., Hill, E. A., McLean, J. S., Jarman, K., Gorby, Y. A., Valentine, N., et al. (2005). Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on matrix assisted laser desorption/ionization whole cell protein fingerprints. J. Microbiol. Methods 62, 259-271. doi: 10.1016/j.mimet.2005.04.033
191. Yaman, G., Akyar, I., and Can, S. (2012). Evaluation of the MALDI TOF-MS method for identification of Candida strains isolated from blood cultures. Diagn. Microbiol. Infect. Dis. 73, 65-67. doi: 10.1016/j.diagmicrobio.2012.01.013
192. Yates, J. R. III. (1998). Mass spectrometry and the age of the proteome. J. Mass Spectrom. 33, 1-19. doi: 10.1002/(SICI)1096-9888(199801)33:1<1::AID-JMS624>3.0.CO;2-9
193. Yi, X., Li, J., Yu, S., Zhang, A., Xu, J., Yi, J., et al. (2011). A new PCR-based mass spectrometry system for high-risk HPV, part I: methods. Am. J. Clin. Pathol. 136, 913-919. doi: 10.1309/AJCPWTZDT0Q7DOVI
194. Yssouf, A., Parola, P., Lindström, A., Lilja, T., L'Ambert, G., and Bondesson, U. (2014). Identification of European mosquito species by MALDI-TOF MS. Parasitol. Res. 113, 2375-2378. doi: 10.1007/s00436-014-3876-y
195. Zaluga, J., Heylen, K., Van Hoorde, K., Hoste, B., Van Vaerenbergh, J., Maes, M., et al. (2011). GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter. Syst. Appl. Microbiol. 34, 400-407. doi: 10.1016/j.syapm.2011.05.001
196. Zhu, S., Ratering, S., Schnell, S., and Wacker, R. (2011). Matrix-assisted laser desorption and ionization-time-of-flight mass spectrometry, 16S rRNA gene sequencing, and API 32E for identification of Cronobacter spp.: a comparative study. J. Food Prot. 74, 2182-2187. doi: 10.4315/0362-028X.JFP-11-205
197. Zürcher, S., Mooser, C., Lüthi, A. U., Mühlemann, K., Barbani, M. T., Mohacsi, P., et al. (2012). Sensitive and rapid detection of ganciclovir resistance by PCR based MALDI-TOF analysis. J. Clin. Virol. 54, 359-363. doi: 10.1016/j.jcv.2012.04.019