Speciation of coagulase negative staphylococci, isolated from indoor air, using SDS page gel bands of expressed proteins followed by MALDI TOF MS and MALDI TOF-TOF MS-MS analysis of tryptic peptides

Journal of Microbiological Methods

Volumn 84, Issue 2, 2011, Pages 243-250

  Fox, Karen ^a   Fox, Alvin ^a   Rose, John ^b   Walla, Michael ^c  

^a UNIVERSITY OF SOUTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b University of South Carolina   (United States)

^c UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

MALDI TOF MS; MALDI TOFTOF MS MS; Mass spectrometry; Proteomics; Tandem mass spectrometry

Indexed keywords

ACONITE HYDRATASE; BACTERIAL PROTEIN; HYDROLYASE; TRYPTIC PEPTIDE; UNCLASSIFIED DRUG;

AMBIENT AIR; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; COAGULASE NEGATIVE STAPHYLOCOCCUS; COMPUTER ANALYSIS; CONTROLLED STUDY; GENETIC CONSERVATION; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; SCHOOL; SEQUENCE ANALYSIS; SPECIES COMPARISON; SPECIES DIFFERENTIATION; TANDEM MASS SPECTROMETRY;

AIR MICROBIOLOGY; BACTERIAL PROTEINS; BACTERIOLOGICAL TECHNIQUES; ELECTROPHORESIS, POLYACRYLAMIDE GEL; PROTEOME; SCHOOLS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; STAPHYLOCOCCUS;

BACTERIA (MICROORGANISMS); STAPHYLOCOCCUS;

EID: 79251619850     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2010.12.007     Document Type: Article

References (41)

1. Baker J. Comparison of various methods for differentiation of staphylococci and micrococci. J. Clin. Microbiol. 1984, 19:875-879.
2. Brodie E., DeSantis T., Parker J., Zubietta I., Piceno Y., Andersen G. Urban aerosols harbor diverse and dynamic bacterial populations. PNAS 2007, 104:299-304.
3. Cain T., Lubman D., Weber J. Differentiation of bacteria using protein profiles from matrix assisted laser desorption/ionization time of flight mass spectrometry. Rapid Commun. Mass Spectrom. 1994, 8:1026-1030.
4. Callahan C., Fox K., Fox A. The small acid soluble proteins of Bacillus weihenstephanensis and Bacillus mycoides group 2 are the most distinct among the Bacillus cereus group. Mol. Cell. Probes 2009, 23:291-297.
5. Castanha E., Fox A., Fox K. Rapid discrimination of Bacillus anthracis from other members of the B. cereus group by mass and sequence of "intact" small acid soluble proteins (SASPs) using mass spectrometry. J. Microbiol. Meth. 2006, 67:230-240.
6. Castanha E., Vestal M., Hattan S., Fox A., Fox K., Dickinson D. Bacillus cereus strains fall into two clusters (one closely and one more distantly related) to Bacillus anthracis according to amino acid substitutions in small acid-soluble proteins as determined by tandem mass spectrometry. Mol. Cell. Probes 2007, 21:190-201.
7. Claydon M., Davey S., Edwards-Jones V., Gordon D. The rapid identification of intact microorganisms using mass spectrometry. Nat. Biotechnol. 1996, 14:1584-1586.
8. Demirev P., Ramirez J., Fenselau C. Tandem mass spectrometry of intact proteins for characterization of biomarkers from Bacillus cereus T spores. Anal. Chem. 2001, 73:5725-5731.
9. Field Guide for the Determination of Biological Contaminants in Environmental Samples 1996, Amer. Indust. Hyg. Assoc., Fairfax, VA. H. Dillon, P. Heinsohn, D. Miller (Eds.).
10. Eng J., McCormack A., Yates J. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Mass Spectrom. 1994, 5:976-989.
11. Everley R., Mott T., Toney D., Croley T. Characterization of Clostridium species utilizing liquid chromatography/mass spectrometry of intact proteins. J. Microbiol. Meth. 2009, 77:152-158.
12. 2 in occupied school rooms. J. Environ. Monit. 2003, 5:1-8.
13. Fox A., Harley W., Feigley C., Salzberg D., Toole C., Sebastian A., Larsson L. Large particles are responsible for elevated bacterial marker levels in school air upon occupation. J. Environ. Monit. 2005, 7:450-456.
14. Fox K., Castanha E., Fox A., Feigley C., Salzberg C. Human K10 epithelial keratin is the most abundant protein in airborne dust of both occupied and unoccupied school rooms. J. Environ. Monit. 2008, 10:55-59.
15. Fox K., Fox A., Elßner T., Feigley C., Salzberg D. MALDI TOF mass spectrometry speciation of staphylococci and their discrimination from micrococci isolated from indoor air of school rooms. J. Environ. Monit. 2010, 12:917-923.
16. François P., Scherl A., Hochstrasser D., Schrenzel J.Review Proteomic approaches to study Staphylococcus aureus pathogenesis. J. Proteomics 2010, 73:701-708.
17. Freiwald, A, Sauer, S. 2009. Phylogenetic classification and identification of bacteria by mass spectrometry 4, 733-742.
18. Gentzel M., Köcher T., Ponnusamy S., Wilm M. Preprocessing of tandem mass spectrometric data to support automatic protein identification. Proteomics 2003, 1597-1610.
19. Hartman E., Colquhoun D., Halden R. Identification of putative biomarkers for toluene-degrading burkholderia and pseudomonads by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and peptide mass finger-printing. Biosci. Biotechnol. Biochem. 2010, 74:1470-1472.
20. Holland R., Wilkes J., Rafii F., Sutherland J., Persons C., Voorhees K., Lay J. Rapid identification of intact whole bacteria based on spectral patterns using matrix assisted laser desorption/ionization with time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom. 1996, 10:1227-1232.
21. Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V., Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M., Goltsman E., Larsen N., D'Souza M., Walunas T., Grechkin Y., Pusch P., Haselkorn R., Fonstein M., Ehrlich S., Overbeek R., Kyrpides N. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 2003, 423:87-89.
22. Iwase T., Seki K., Shinji H., Mizunoe Y., Masuda S. Development of a real-time PCR assay for the detection and identification of Staphylococcus capitis, Staphylococcus haemolyticus and Staphylococcus warneri. J. Med. Microbiol. 2007, 56:1346-1349.
23. Jabbour R., Deshpande V., Wade M., Stanford M., Wick C., Zulich A., Skowronski E., Snyder P. Double-blind characterization of non-genome-sequenced bacteria by mass spectrometry-based proteomics. Appl. Environ. Microbiol. 2010, 76:3637-3644.
24. Jabbour R., Wade M., Deshpande S., Stanford M., Wick C., Zulich A., Snyder P. Identification of Yersinia pestis and Escherichia coli strains by whole cell and outer membrane protein extracts with mass spectrometry-based proteomics. J. Proteome Res. 2010, 2010(9):3647-3655.
25. Krishnamurphy T., Ross P., Rajamani U. Detection of pathogenic and non-pathogenic bacteria by matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Meth. Commun. Mass Spectrom. 1996, 10:883-888.
26. Lai M., Phadke N., Kachman M., Giorno R., Vazquez S., Vazquez J., Maddock J., Driks A. Proteomic analysis of the spore coats of Bacillus subtilis and Bacillus anthracis. J. Bacteriol. 2003, 185:1443-1454.
27. Lee S., Berger S., Martinovic S., Paša-Tolic L., Anderson G., Shen Y., Zhao R., Smith R. Direct mass spectrometric analysis of intact proteins of the yeast large ribosomal subunit using capillary LC-FTICR. PNAS 2002, 99:5942-5947.
28. Lis D., Pacha J., Idzik D. Methicillin resistance of airborne coagulase-negative staphylococci in homes of persons having contact with a hospital environment. Am. J. Infect. Control 2009, 37:177-182.
29. Liu H., Bergman N., Thomason B., Shallom S., Hazen A., Crossno J., Rasko D., Ravel J., Read T., Peterson S., Yates J., Hanna P. Formation and composition of the Bacillus anthracis endospore. J. Bacteriol. 2004, 186:164-178.
30. Morgan M., Boyette M., Goforth C., Sperry K., Greene S. Comparison of the Biolog OmniLog identification system and 16S ribosomal RNA gene sequencing for accuracy in identification of atypical bacteria of clinical origin. J. Microbiol. Meth. 2009, 79:333-343.
31. Ogawa M., Renesto P., Azza S., Moinier D., Fourquet P., Gorvel J., Raoult D. Proteome analysis of Rickettsia felis highlights the expression profile of intracellular bacteria. Proteomics 2007, 7:1232-1248.
32. Read T., Salzberg S., Pop M., Shumway M., Umayam L., Jiang L., Holzapple E., Busch J., Smith K., Schupp J., Solomon D., Keim P., Frazer C. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 2002, 296:2028-2033.
33. Renard B., Kirchner M., Monigatti F., Ivanov A., Rappsilber J., Winter D., Steen J., Hamprecht F., Steen H. When less can yield more - computational preprocessing of MS/MS spectra for peptide identification. Proteomics 2009, 9:4978-4984.
34. Shevchenko A., Jensen O., Podtelejnikov A., Sagliocco F., Wilm M., Vorm O., Mortensen P., Shevchenko A., Boucherie H., Mann M. Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:14440-14445.
35. Walker J., Fox A.J., Edwards-Jones V., Gordon D. Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility. J. Microbiol. Meth. 2002, 48:117-126.
36. Walters M., Mobley H. Identification of uropathogenic Escherichia coli surface proteins by shotgun proteomics. J. Microbiol. Meth. 2009, 78:131-135.
37. Ward D., Weller R., Bateson M. 16S rRNA sequences reveal numerous unculturable microorganisms in a natural community. Nature 1990, 345:63-65.
38. Washburne M., Wolters D., Yates J. Large scale analysis of the yeast proteome by multidimensional protein identification technology. Nature 2001, 19:242-247.
39. Weinstein M.P., Mirrett S., Van Pelt L., Mckinnon M., Zimmer B., Kloos W., Reller L. Clinical importance of identifying coagulase-negative staphylococci isolated from blood cultures: evaluation of MicroScan rapid and dried overnight Gram-positive panels versus a conventional reference method. J. Clin. Microbiol. 1998, 36:2089-2092.
40. Wilson M. Bacteriology of Humans 2008, Blackwell Publishing, Malden, MA.
41. Wynne C., Fenselau C., Demirev P., Edwards N. Top-down identification of protein biomarkers in bacteria with unsequenced genomes. Anal. Chem. 2009, 81:9633-9642.