Sample handling and mass spectrometry for microbial metaproteomic analyses

Methods in Enzymology

Volumn 531, Issue , 2013, Pages 289-303

  Mueller, Ryan S ^a   Pan, Chongle ^b  

^a OREGON STATE UNIVERSITY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Mass spectrometry; Metaproteomics; Microbial communities; Microbial ecology; MS proteomics; Proteomics

Indexed keywords

AMINO ACID; PEPTIDE; PROTEOME;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ANIMAL CELL; ARTICLE; BIODIVERSITY; CATION EXCHANGE; CONTROLLED STUDY; CYTOLYSIS; DNA SEQUENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; LIMIT OF QUANTITATION; LIQUID CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY; MASS SPECTROMETER; MASS SPECTROMETRY; MATERIALS HANDLING; MEASUREMENT; METAPROTEOMICS; MICROBIAL BIOMASS; MICROBIAL COMMUNITY; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; SOLUBILIZATION; STRONG CATION EXCHANGE; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TANDEM MASS SPECTROMETRY;

KEYWORDS; MASS SPECTROMETRY; METAPROTEOMICS; MICROBIAL COMMUNITIES; MICROBIAL ECOLOGY; MS PROTEOMICS; PROTEOMICS;

BACTERIA; CHROMATOGRAPHY, LIQUID; MASS SPECTROMETRY; METAGENOME; MICROBIAL CONSORTIA; PROTEOME; SPECIMEN HANDLING;

EID: 84884552483     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-407863-5.00015-0     Document Type: Chapter

References (60)

1. F. Abram, A.-M. Enright, J. O'Reilly, C.H. Botting, G. Collins, and V. O'Flaherty A metaproteomic approach gives functional insights into anaerobic digestion Journal of Applied Microbiology 110 2011 1550 1560
2. M. Bantscheff, S. Lemeer, M.M. Savitski, and B. Kuster Quantitative mass spectrometry in proteomics: Critical review update from 2007 to the present Analytical and Bioanalytical Chemistry 404 2012 939 965
3. M. Bantscheff, M. Schirle, G. Sweetman, J. Rick, and B. Kuster Quantitative mass spectrometry in proteomics: A critical review Analytical and Bioanalytical Chemistry 389 2007 1017 1031
4. C.P. Belnap, C. Pan, N.C. VerBerkmoes, M.E. Power, N.F. Samatova, and R. Carver Cultivation and quantitative proteomic analyses of acidophilic microbial communities The ISME Journal 4 2009 520 530
5. R.J. Benyon, M.K. Doherty, J.M. Pratt, and S.J. Gaskell Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides Nature Methods 2 2005 587 589
6. K.E. Burnhum, S.J. Callister, C.D. Nicora, S.O. Purvine, P. Hugenholz, and F. Warnecke Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome The ISME Journal 5 2011 161 164
7. Y.C. Chen, J. Shiea, and J. Sunner Thin-layer chromatography-mass spectrometry using activated carbon, surface-assisted laser desorption/ ionization Journal of Chromatography. A 826 1998 77 86
8. K. Chourey, J. Jansson, N. VerBerkmoes, M. Shah, K.L. Chavarria, and L.M. Tom Direct cellular lysis/protein extraction protocol for soil metaproteomics Journal of Proteome Research 9 2010 6615 6622
9. N. Delmotte, C. Knief, S. Chaffron, G. Innerebner, B. Roschitzki, and R. Schlapbach Community proteogenomics reveals insights into the physiology of phyllosphere bacteria Proceedings of the National Academy of Sciences of the United States of America 106 2009 16428 16433
10. V.J. Denef, and J.F. Banfield In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids Science 336 2012 462 466
11. V.J. Denef, L.H. Kalnejais, R.S. Mueller, P. Wilmes, B.J. Baker, and B.C. Thomas Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities Proceedings of the National Academy of Sciences of the United States of America 107 2010 2383 2390
12. S. Di Palma, P.J. Boersema, A.J.R. Heck, and S. Mohammed Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis Analytical Chemistry 83 2011 3440 3447
13. B.K. Erickson, R.S. Mueller, N.C. VerBerkmoes, M. Shah, S.W. Singer, and M. Thelen Computational prediction and experimental validation of signal peptide cleavages in the extracellular proteome of a natural microbial community Journal of Proteome Research 9 2010 2148 2159
14. J.B. Fenn, M. Mann, C.K. Meng, S.F. Wong, and C.M. Whitehouse Electrospray ionization for mass spectrometry of large biomolecules Science 246 1989 64 71
15. S.B. Ficarro, M.L. McCleland, P.T. Stukenber, D.J. Burke, M.M. Ross, and J. Shabanowitz Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nature Biotechnology 20 2002 301 305
16. L. Florens, M.J. Carozza, S.K. Swanson, M. Fournier, M.K. Coleman, and J.L. Workman Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors Methods 40 2006 303 311
17. R. Fukuda, H. Ogawa, T. Nagata, and I. Koike Direct determination of carbon and nitrogen contents of natural bacterial assemblages in marine environments Applied and Environmental Microbiology 64 1998 3352 3358
18. S.A. Gerber, J. Rush, O. Stemman, M.W. Kirschner, and S.P. Gygi Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS Proceedings of the National Academy of Sciences of the United States of America 100 2003 6940 6945
19. N.M. Griffin, J. Yu, F. Long, P. Oh, S. Shore, and Y. Li Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis Nature Biotechnology 28 2010 83 89
20. N. Gupta, S. Tanner, N. Jaitly, J.N. Adkins, M. Lipton, and R. Edwards Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation Genome Research 17 2007 1362 1377
21. S.-B. Haange, A. Oberbach, N. Schlichting, F. Hugenholz, H. Smidt, and M. von Bergen Metaproteome analysis and molecular genetics of rat intestinal microbiota reveals section and localization resolved species distribution and enzymatic functionalities Journal of Proteome Research 11 2012 5406 5417
22. P. Hörth, C.A. Miller, T. Preckel, and C. Wenz Efficient fractionation and improved protein identification by peptide OFFGEL electrophoresis Molecular & Cellular Proteomics 5 2006 1968 1974
23. M. Jafari, V. Primo, G.B. Smejkal, E.V. Moskovets, W.P. Kuo, and A.R. Ivanov Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling Electrophoresis 33 2012 2516 2526
24. J.D. Jaffe, H.C. Berg, and G.M. Church Proteogenomic mapping as a complementary method to perform genome annotation Proteomics 4 2003 59 77
25. N.B. Justice, C. Pan, R.S. Mueller, S.E. Spaulding, V. Shah, and C.L. Sun Heterotropic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities Applied and Environmental Microbiology 78 2012 8321 8330
26. M. Karas, and F. Hillenkamp Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons Analytical Chemistry 60 1988 2299 2301
27. K.M. Keiblinger, I.C. Wilhartitz, T. Schneider, B. Roschitzki, E. Schmid, and L. Eberl Soil metaproteomics - Comparative evaluation of protein extraction protocols Soil Biology & Biogeochemistry 54 2012 14 24
28. E.S. Klaassens, W.M. de Vos, and E.E. Vaughan Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract Applied and Environmental Microbiology 73 2007 1388 1392
29. C.M.R. Lacerda, L.H. Choe, and K.F. Reardon Metaproteomic analysis of a bacterial community response to cadmium exposure Journal of Proteome Research 6 2007 1145 1152
30. V.V. Laiko, M.A. Baldwin, and A.L. Burlingame Atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry Analytical Chemistry 72 2000 652 657
31. Z. Li, R.M. Adams, K. Chourey, G.B. Hurst, R.L. Hettich, and C. Pan Systematic comparison of label-free, metabolic labeling, and isobaric labeling for quantitative proteomics on LTQ orbitrap velos Journal of Proteome Research 11 2011 1582 1590
32. A.J. Link, J. Eng, D.M. Schieltz, E. Carmack, G.J. Mize, and D.R. Morris Direct analysis of protein complexes using mass spectrometry Nature Biotechnology 17 1999 676 682
33. M. Liu, L. Fan, L. Zhong, S. Kjelleberg, and T. Thomas Metaproteomic analysis of a community of sponge symbionts The ISME Journal 6 2012 1515 1525
34. L.L. Manza, S.L. Stamer, A.J. Ham, S.G. Codreanu, and D.C. Liebler Sample preparation and digestion for proteomic analyses using spin filters Proteomics 5 2005 1742 1745
35. W.H. McDonald, R. Ohi, D.T. Miyamoto, T.J. Mitchison, and J.R. Yates III Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: Single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT International Journal of Mass Spectrometry 219 2002 245 251
36. M. Merchant, and S. Weinberger Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry Electrophoresis 21 2000 1164 1167
37. R.M. Morris, B.L. Nunn, C. Frazar, D.R. Goodlett, Y.S. Ting, and G. Rocap Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction The ISME Journal 4 2010 673 685
38. R.S. Mueller, V.J. Denef, L.H. Kainejais, B. Suttle, B.C. Thomas, and P. Wilmes Ecological distribution and population physiology defined by proteomics in a natural microbial community Molecular Systems Biology 6 2010 1 12
39. R.S. Mueller, B.D. Dill, C. Pan, C. Belnap, B.C. Thomas, and N.C. VerBerkmoes Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community Environmental Microbiology 13 2011 2279 2292
40. P.H. O'Farrell High resolution two-dimensional electrophoresis of proteins The Journal of Biological Chemistry 250 1975 4007 4021
41. S.-E. Ong, B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, and A. Pandey Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Molecular & Cellular Proteomics 1 2002 376 386
42. C. Pan, C. Fischer, D. Hyatt, B. Bowen, R.L. Hettich, and J.F. Banfield Quantitative tracking of isotope flows in proteomes of microbial communities Molecular & Cellular Proteomics 10 2011 1 11
43. C. Pan, G. Kora, W.H. McDonald, D.L. Tabb, N.C. VerBerkmoes, and G.B. Hurst ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation Analytical Chemistry 78 2006 7121 7131
44. R.J. Ram, N.C. VerBerkmoes, M.P. Thelen, G.W. Tyson, B.J. Baker, and R.C. Blake II Community proteomics of a natural microbial biofilm Science 308 2005 1915 1920
45. P.L. Ross, Y.N. Huang, J.N. Marchese, B. Williamson, K. Parker, and S. Hattan Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Molecular & Cellular Proteomics 3 2004 1154 1169
46. A. Savidor, R.S. Donahoo, O. Hurtado-Gonzales, N.C. VerBerkmoes, M.B. Shah, and K.H. Lamour Expressed peptide tags: An additional layer of data for genome annotation Journal of Proteome Research 5 2006 3048 3058
47. T. Schneider, K.M. Kieblinger, E. Schmid, K. Sterflinger-Gleixner, G. Ellersdorfer, and B. Roschitzki Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions The ISME Journal 6 2012 1749 1762
48. S.W. Singer, B.E. Erickson, N.C. VerBerkmoes, M. Hwang, M.B. Shah, and R.L. Hettich Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities The ISME Journal 4 2010 1398 1409
49. M. Taubert, C. Vogt, T. Wubet, S. Kleinsteuber, M.T. Tarkka, and H. Harms Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium The ISME Journal 6 2012 2291 2301
50. J.J. Thomas, Z. Shen, J.E. Crowell, M.G. Finn, and G. Siuzdak Desorption/ionization on silicon (DIOS): A diverse mass spectrometry platform for protein characterization Proceedings of the National Academy of Sciences of the United States of America 98 2001 4932 4937
51. A. Thompson, J. Schäfer, K. Kuhn, S. Kienle, J. Schwarz, and G. Schmidt Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS Analytical Chemistry 75 2003 1895 1904
52. N.C. Verberkmoes, A.L. Russell, M. Shah, A. Godzik, M. Rosenquist, and J. Halfvarson Shotgun metaproteomics of the human distal gut microbiota The ISME Journal 3 2009 179 189
53. M.J. Wilkins, N.C. VerBerkmoes, K.H. William, S.J. Callister, P.J. Mouser, and H. Elifantz Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation Applied and Environmental Microbiology 75 2009 6591 6599
54. T.J. Williams, E. Long, F. Evans, M.Z. DeMaere, F.M. Lauro, and M.J. Raferty A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters The ISME Journal 6 2012 1883 1900
55. P. Wilmes, M. Wexler, and P.L. Bond Metaproteomics provides functional insight into activated sludge wastewater treatment PloS One 3 2008 e1778
56. J.R. Wiśnewski, N. Nagaraj, A. Zougman, F. Gnad, and M. Mann Brain phosphoproteome obtained by FASP-based method reveals plasma membrane protein topology Journal of Proteome Reasearch 9 2010 3280 3289
57. J.R. Wiśnewski, A. Zougman, N. Nagaraj, and M. Mann Universal sample preparation method for proteome analysis Nature Methods 6 2009 359 363
58. D.A. Wolters, M.P. Washburn, and J.R. Yates III An automated multidimensional protein identification technology for shotgun proteomics Analytical Chemistry 73 2001 5683 5690
59. J.R. Yates III, C.I. Ruse, and A. Nakorchevsky Proteomics by mass spectrometry: Approaches, advances, and applications Annual Review of Biomedical Engineering 11 2009 49 79
60. M.V. Zubkov, B.M. Fuchs, H. Eilers, P.H. Burkill, and R. Amann Determination of total protein content of bacterial cells by SYPRO staining and flow cytometry Applied and Environmental Microbiology 65 1999 3251 3257