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Volumn 8, Issue 12, 2013, Pages

Evaluating the impact of different sequence databases on metaproteome analysis: Insights from a lab-assembled microbial mixture

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM; EUKARYOTE; METAGENOMICS; METAPROTEOMICS; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEOMICS; RELIABILITY; SEQUENCE ANALYSIS; SEQUENCE DATABASE; TAXONOMY; BACTERIA; COMPARATIVE STUDY; GENETICS; MICROBIAL CONSORTIUM; PROCEDURES;

EID: 84891938742     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0082981     Document Type: Article
Times cited : (94)

References (76)
  • 1
    • 84861961018 scopus 로고    scopus 로고
    • Tackling the microbiome
    • Hood L (2012) Tackling the microbiome. Science 336: 1209.
    • (2012) Science , vol.336 , pp. 1209
    • Hood, L.1
  • 2
    • 77956647726 scopus 로고    scopus 로고
    • Systems approaches to microbial communities and their functioning
    • Roling WF, Ferrer M, Golyshin PN (2010) Systems approaches to microbial communities and their functioning. Curr Opin Biotechnol 21: 532-538.
    • (2010) Curr Opin Biotechnol , vol.21 , pp. 532-538
    • Roling, W.F.1    Ferrer, M.2    Golyshin, P.N.3
  • 3
    • 84876403132 scopus 로고    scopus 로고
    • Going local: Technologies for exploring bacterial microenvironments
    • Wessel AK, Hmelo L, Parsek MR, Whiteley M (2013) Going local: technologies for exploring bacterial microenvironments. Nat Rev Microbiol 11: 337-348.
    • (2013) Nat Rev Microbiol , vol.11 , pp. 337-348
    • Wessel, A.K.1    Hmelo, L.2    Parsek, M.R.3    Whiteley, M.4
  • 4
    • 84864587851 scopus 로고    scopus 로고
    • Interspecific interactions in mixed microbial cultures in a biodegradation perspective
    • Mikeskova H, Novotny C, Svobodova K (2012) Interspecific interactions in mixed microbial cultures in a biodegradation perspective. Appl Microbiol Biotechnol 95: 861-870.
    • (2012) Appl Microbiol Biotechnol , vol.95 , pp. 861-870
    • Mikeskova, H.1    Novotny, C.2    Svobodova, K.3
  • 5
    • 84862170733 scopus 로고    scopus 로고
    • Modeling microbial communities: Current, developing, and future technologies for predicting microbial community interaction
    • Larsen P, Hamada Y, Gilbert J (2012) Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction. J Biotechnol 160: 17-24.
    • (2012) J Biotechnol , vol.160 , pp. 17-24
    • Larsen, P.1    Hamada, Y.2    Gilbert, J.3
  • 6
    • 84861997084 scopus 로고    scopus 로고
    • Microbial communities involved in enhanced biological phosphorus removal from wastewater-A model system in environmental biotechnology
    • Nielsen PH, Saunders AM, Hansen AA, Larsen P, Nielsen JL (2012) Microbial communities involved in enhanced biological phosphorus removal from wastewater-a model system in environmental biotechnology. Curr Opin Biotechnol 23: 452-459.
    • (2012) Curr Opin Biotechnol , vol.23 , pp. 452-459
    • Nielsen, P.H.1    Saunders, A.M.2    Hansen, A.A.3    Larsen, P.4    Nielsen, J.L.5
  • 7
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium
    • Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 8
    • 84858439578 scopus 로고    scopus 로고
    • The human microbiome: At the interface of health and disease
    • Cho I, Blaser MJ (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13: 260-270.
    • (2012) Nat Rev Genet , vol.13 , pp. 260-270
    • Cho, I.1    Blaser, M.J.2
  • 10
    • 10944226351 scopus 로고    scopus 로고
    • Metagenomics: Genomic analysis of microbial communities
    • DOI 10.1146/annurev.genet.38.072902.091216
    • Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38: 525-552. (Pubitemid 40013737)
    • (2004) Annual Review of Genetics , vol.38 , pp. 525-552
    • Riesenfeld, C.S.1    Schloss, P.D.2    Handelsman, J.3
  • 11
    • 52949115612 scopus 로고    scopus 로고
    • Microbiology: Metagenomics
    • Hugenholtz P, Tyson GW (2008) Microbiology: metagenomics. Nature 455: 481-483.
    • (2008) Nature , vol.455 , pp. 481-483
    • Hugenholtz, P.1    Tyson, G.W.2
  • 13
    • 84868091529 scopus 로고    scopus 로고
    • Metagenomics: Microbial diversity through a scratched lens
    • Temperton B, Giovannoni SJ (2012) Metagenomics: microbial diversity through a scratched lens. Curr Opin Microbiol 15: 605-612.
    • (2012) Curr Opin Microbiol , vol.15 , pp. 605-612
    • Temperton, B.1    Giovannoni, S.J.2
  • 15
    • 31944437874 scopus 로고    scopus 로고
    • Metaproteomics: Studying functional gene expression in microbial ecosystems
    • DOI 10.1016/j.tim.2005.12.006, PII S0966842X05003379
    • Wilmes P, Bond PL (2006) Metaproteomics: studying functional gene expression in microbial ecosystems. Trends Microbiol 14: 92-97. (Pubitemid 43190739)
    • (2006) Trends in Microbiology , vol.14 , Issue.2 , pp. 92-97
    • Wilmes, P.1    Bond, P.L.2
  • 16
  • 17
    • 84859573112 scopus 로고    scopus 로고
    • Exploring mixed microbial community functioning: Recent advances in metaproteomics
    • Siggins A, Gunnigle E, Abram F (2012) Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 80: 265-280.
    • (2012) FEMS Microbiol Ecol , vol.80 , pp. 265-280
    • Siggins, A.1    Gunnigle, E.2    Abram, F.3
  • 18
    • 84864035417 scopus 로고    scopus 로고
    • Microbial metaproteomics: Identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities
    • Hettich RL, Sharma R, Chourey K, Giannone RJ (2012) Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities. Curr Opin Microbiol 15: 373-380.
    • (2012) Curr Opin Microbiol , vol.15 , pp. 373-380
    • Hettich, R.L.1    Sharma, R.2    Chourey, K.3    Giannone, R.J.4
  • 19
    • 84874875475 scopus 로고    scopus 로고
    • Searching for a needle in a stack of needles: Challenges in metaproteomics data analysis
    • Muth T, Benndorf D, Reichl U, Rapp E, Martens L (2013) Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. Mol Biosyst 9: 578.
    • (2013) Mol Biosyst , vol.9 , pp. 578
    • Muth, T.1    Benndorf, D.2    Reichl, U.3    Rapp, E.4    Martens, L.5
  • 20
    • 84885076723 scopus 로고    scopus 로고
    • Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
    • Seifert J, Herbst FA, Nielsen PH, Planes FJ, Ferrer M, et al. (2013) Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities. Proteomics 13: 2786-2804.
    • (2013) Proteomics , vol.13 , pp. 2786-2804
    • Seifert, J.1    Herbst, F.A.2    Nielsen, P.H.3    Planes, F.J.4    Ferrer, M.5
  • 21
    • 84876532610 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • NCBI Resource Coordinators
    • NCBI Resource Coordinators (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 41: D8-D20.
    • (2013) Nucleic Acids Res , vol.41
  • 22
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • UniProt Consortium
    • UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40: D71-75.
    • (2012) Nucleic Acids Res , vol.40 , pp. 71-75
  • 24
    • 0035326344 scopus 로고    scopus 로고
    • Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching
    • DOI 10.1021/ac0013709
    • Shevchenko A, Sunyaev S, Loboda A, Bork P, Ens W, et al. (2001) Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching. Anal Chem 73: 1917-1926. (Pubitemid 32862395)
    • (2001) Analytical Chemistry , vol.73 , Issue.9 , pp. 1917-1926
    • Shevchenko, A.1    Sunyaev, S.2    Loboda, A.3    Shevchenko, A.4    Bork, P.5    Ens, W.6    Standing, K.G.7
  • 26
    • 33751068791 scopus 로고    scopus 로고
    • Performance evaluation of existing de novo sequencing algorithms
    • DOI 10.1021/pr060222h
    • Pevtsov S, Fedulova I, Mirzaei H, Buck C, Zhang X (2006) Performance evaluation of existing de novo sequencing algorithms. J Proteome Res 5: 3018-3028. (Pubitemid 44754676)
    • (2006) Journal of Proteome Research , vol.5 , Issue.11 , pp. 3018-3028
    • Pevtsov, S.1    Fedulova, I.2    Mirzaei, H.3    Buck, C.4    Zhang, X.5
  • 28
    • 58549091696 scopus 로고    scopus 로고
    • Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation
    • Denef VJ, VerBerkmoes NC, Shah MB, Abraham P, Lefsrud M, et al. (2009) Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol 11: 313-325.
    • (2009) Environ Microbiol , vol.11 , pp. 313-325
    • Denef, V.J.1    Verberkmoes, N.C.2    Shah, M.B.3    Abraham, P.4    Lefsrud, M.5
  • 29
    • 70349481520 scopus 로고    scopus 로고
    • Community proteogenomics reveals insights into the physiology of phyllosphere bacteria
    • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, et al. (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci U S A 106: 16428-16433.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 16428-16433
    • Delmotte, N.1    Knief, C.2    Chaffron, S.3    Innerebner, G.4    Roschitzki, B.5
  • 30
    • 81755176064 scopus 로고    scopus 로고
    • Strategies for metagenomic-guided whole-community proteomics of complex microbial environments
    • Cantarel BL, Erickson AR, VerBerkmoes NC, Erickson BK, Carey PA, et al. (2011) Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. PLoS One 6: e27173.
    • (2011) PLoS One , vol.6
    • Cantarel, B.L.1    Erickson, A.R.2    Verberkmoes, N.C.3    Erickson, B.K.4    Carey, P.A.5
  • 31
    • 78650780115 scopus 로고    scopus 로고
    • An iterative workflow for mining the human intestinal metaproteome
    • Rooijers K, Kolmeder C, Juste C, Doré J, de Been M, et al. (2011) An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 12: 6.
    • (2011) BMC Genomics , vol.12 , pp. 6
    • Rooijers, K.1    Kolmeder, C.2    Juste, C.3    Doré, J.4    De Been, M.5
  • 32
    • 84870322666 scopus 로고    scopus 로고
    • Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease
    • Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, et al. (2012) Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One 7: e49138.
    • (2012) PLoS One , vol.7
    • Erickson, A.R.1    Cantarel, B.L.2    Lamendella, R.3    Darzi, Y.4    Mongodin, E.F.5
  • 33
    • 84871933045 scopus 로고    scopus 로고
    • Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure
    • Ferrer M, Ruiz A, Lanza F, Haange SB, Oberbach A, et al. (2013) Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure. Environ Microbiol 15: 211-226.
    • (2013) Environ Microbiol , vol.15 , pp. 211-226
    • Ferrer, M.1    Ruiz, A.2    Lanza, F.3    Haange, S.B.4    Oberbach, A.5
  • 34
    • 84860854996 scopus 로고    scopus 로고
    • Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium
    • Morris BE, Herbst FA, Bastida F, Seifert J, von Bergen M, et al. (2012) Microbial interactions during residual oil and n-fatty acid metabolism by a methanogenic consortium. Environ Microbiol Rep 4: 297-306.
    • (2012) Environ Microbiol Rep , vol.4 , pp. 297-306
    • Morris, B.E.1    Herbst, F.A.2    Bastida, F.3    Seifert, J.4    Von Bergen, M.5
  • 36
    • 77951497989 scopus 로고    scopus 로고
    • Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction
    • Morris RM, Nunn BL, Frazar C, Goodlett DR, Ting YS, et al. (2010) Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction. ISME J 4: 673-685.
    • (2010) ISME J , vol.4 , pp. 673-685
    • Morris, R.M.1    Nunn, B.L.2    Frazar, C.3    Goodlett, D.R.4    Ting, Y.S.5
  • 39
    • 84885072320 scopus 로고    scopus 로고
    • Proteogenomics for environmental microbiology
    • Armengaud J, Hartmann EM, Bland C (2013) Proteogenomics for environmental microbiology. Proteomics 13: 2731-2742.
    • (2013) Proteomics , vol.13 , pp. 2731-2742
    • Armengaud, J.1    Hartmann, E.M.2    Bland, C.3
  • 40
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • DOI 10.1038/nmeth1019, PII NMETH1019
    • Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4: 207-214. (Pubitemid 46358868)
    • (2007) Nature Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 41
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • DOI 10.1021/ac025747h
    • Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74: 5383-5392. (Pubitemid 35215372)
    • (2002) Analytical Chemistry , vol.74 , Issue.20 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 42
    • 77953016667 scopus 로고    scopus 로고
    • Estimating the confidence of peptide identifications without decoy databases
    • Renard BY, Timm W, Kirchner M, Steen JA, Hamprecht FA, et al. (2010) Estimating the confidence of peptide identifications without decoy databases. Anal Chem 82: 4314-4318.
    • (2010) Anal Chem , vol.82 , pp. 4314-4318
    • Renard, B.Y.1    Timm, W.2    Kirchner, M.3    Steen, J.A.4    Hamprecht, F.A.5
  • 44
    • 79952309062 scopus 로고    scopus 로고
    • Quality assessments of peptide-spectrum matches in shotgun proteomics
    • Granholm V, Kall L (2011) Quality assessments of peptide-spectrum matches in shotgun proteomics. Proteomics 11: 1086-1093.
    • (2011) Proteomics , vol.11 , pp. 1086-1093
    • Granholm, V.1    Kall, L.2
  • 45
    • 82755181910 scopus 로고    scopus 로고
    • Analysis of the resolution limitations of peptide identification algorithms
    • Colaert N, Degroeve S, Helsens K, Martens L (2011) Analysis of the resolution limitations of peptide identification algorithms. J Proteome Res 10: 5555-5561.
    • (2011) J Proteome Res , vol.10 , pp. 5555-5561
    • Colaert, N.1    Degroeve, S.2    Helsens, K.3    Martens, L.4
  • 46
    • 84868310579 scopus 로고    scopus 로고
    • Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies
    • Blakeley P, Overton IM, Hubbard SJ (2012) Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J Proteome Res 11: 5221-5234.
    • (2012) J Proteome Res , vol.11 , pp. 5221-5234
    • Blakeley, P.1    Overton, I.M.2    Hubbard, S.J.3
  • 47
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • DOI 10.1074/mcp.R500012-MCP200
    • Nesvizhskii AI, Aebersold R (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics 4: 1419-1440. (Pubitemid 41555469)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.10 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 48
    • 84869211929 scopus 로고    scopus 로고
    • Inference and validation of protein identifications
    • Claassen M (2012) Inference and validation of protein identifications. Mol Cell Proteomics 11: 1097-1104.
    • (2012) Mol Cell Proteomics , vol.11 , pp. 1097-1104
    • Claassen, M.1
  • 49
    • 84892837034 scopus 로고    scopus 로고
    • Metaproteomics of our microbiome - Developing insight in function and activity in man and model systems
    • In press
    • Kolmeder CA, de Vos WM (2013) Metaproteomics of our microbiome - Developing insight in function and activity in man and model systems. J Proteomics In press.
    • (2013) J Proteomics
    • Kolmeder, C.A.1    De Vos, W.M.2
  • 50
    • 33847702910 scopus 로고    scopus 로고
    • MEGAN analysis of metagenomic data
    • DOI 10.1101/gr.5969107
    • Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386. (Pubitemid 46376747)
    • (2007) Genome Research , vol.17 , Issue.3 , pp. 377-386
    • Huson, D.H.1    Auch, A.F.2    Qi, J.3    Schuster, S.C.4
  • 51
    • 84860162730 scopus 로고    scopus 로고
    • Introduction to the analysis of environmental sequences: Metagenomics with MEGAN
    • Huson DH, Mitra S (2012) Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN. Methods Mol Biol 856: 415-429.
    • (2012) Methods Mol Biol , vol.856 , pp. 415-429
    • Huson, D.H.1    Mitra, S.2
  • 53
    • 76149096479 scopus 로고    scopus 로고
    • A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry
    • Rudney JD, Xie H, Rhodus NL, Ondrey FG, Griffin TJ (2010) A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol Oral Microbiol 25: 38-49.
    • (2010) Mol Oral Microbiol , vol.25 , pp. 38-49
    • Rudney, J.D.1    Xie, H.2    Rhodus, N.L.3    Ondrey, F.G.4    Griffin, T.J.5
  • 54
    • 84870936792 scopus 로고    scopus 로고
    • Unipept: Tryptic Peptide-based biodiversity analysis of metaproteome samples
    • Mesuere B, Devreese B, Debyser G, Aerts M, Vandamme P, et al. (2012) Unipept: tryptic Peptide-based biodiversity analysis of metaproteome samples. J Proteome Res 11: 5773-5780.
    • (2012) J Proteome Res , vol.11 , pp. 5773-5780
    • Mesuere, B.1    Devreese, B.2    Debyser, G.3    Aerts, M.4    Vandamme, P.5
  • 55
    • 3042661951 scopus 로고    scopus 로고
    • Rapid isolation of yeast genomic DNA: Bust n' Grab
    • Harju S, Fedosyuk H, Peterson KR (2004) Rapid isolation of yeast genomic DNA: Bust n' Grab. BMC Biotechnol 4: 8.
    • (2004) BMC Biotechnol , vol.4 , pp. 8
    • Harju, S.1    Fedosyuk, H.2    Peterson, K.R.3
  • 56
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • DOI 10.1101/gr.074492.107
    • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829. (Pubitemid 351645072)
    • (2008) Genome Research , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 57
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identification
    • Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.L.2    Locascio, P.F.3    Land, M.L.4    Larimer, F.W.5
  • 59
    • 78649854658 scopus 로고    scopus 로고
    • Direct cellular lysis/protein extraction protocol for soil metaproteomics
    • Chourey K, Jansson J, VerBerkmoes N, Shah M, Chavarria KL, et al. (2010) Direct cellular lysis/protein extraction protocol for soil metaproteomics. J Proteome Res 9: 6615-6622.
    • (2010) J Proteome Res , vol.9 , pp. 6615-6622
    • Chourey, K.1    Jansson, J.2    Verberkmoes, N.3    Shah, M.4    Chavarria, K.L.5
  • 60
    • 79955372649 scopus 로고    scopus 로고
    • A protein processing filter method for bacterial identification by mass spectrometry-based proteomics
    • Jabbour RE, Deshpande SV, Stanford MF, Wick CH, Zulich AW, et al. (2011) A protein processing filter method for bacterial identification by mass spectrometry-based proteomics. J Proteome Res 10: 907-912.
    • (2011) J Proteome Res , vol.10 , pp. 907-912
    • Jabbour, R.E.1    Deshpande, S.V.2    Stanford, M.F.3    Wick, C.H.4    Zulich, A.W.5
  • 61
    • 84870875533 scopus 로고    scopus 로고
    • Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization
    • Sharma R, Dill BD, Chourey K, Shah M, Verberkmoes NC, et al. (2012) Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization. J Proteome Res 11: 6008-6018.
    • (2012) J Proteome Res , vol.11 , pp. 6008-6018
    • Sharma, R.1    Dill, B.D.2    Chourey, K.3    Shah, M.4    Verberkmoes, N.C.5
  • 62
    • 84883295723 scopus 로고    scopus 로고
    • Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome
    • Tanca A, Biosa G, Pagnozzi D, Addis MF, Uzzau S (2013) Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of the Escherichia coli proteome. Proteomics 13: 2597-2607.
    • (2013) Proteomics , vol.13 , pp. 2597-2607
    • Tanca, A.1    Biosa, G.2    Pagnozzi, D.3    Addis, M.F.4    Uzzau, S.5
  • 63
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wiśniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6: 359-362.
    • (2009) Nat Methods , vol.6 , pp. 359-362
    • Wiśniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 64
    • 84876338400 scopus 로고    scopus 로고
    • Application of 2-D DIGE to formalin-fixed diseased tissue samples from hospital repositories: Results from four case studies
    • Tanca A, Pisanu S, Biosa G, Pagnozzi D, Antuofermo E, et al. (2012) Application of 2-D DIGE to formalin-fixed diseased tissue samples from hospital repositories: results from four case studies. Proteomics Clin Appl 7: 252-263.
    • (2012) Proteomics Clin Appl , vol.7 , pp. 252-263
    • Tanca, A.1    Pisanu, S.2    Biosa, G.3    Pagnozzi, D.4    Antuofermo, E.5
  • 65
    • 67650345724 scopus 로고    scopus 로고
    • Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets
    • Spivak M, Weston J, Bottou L, Kall L, Noble WS (2009) Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets. J Proteome Res 8: 3737-3745.
    • (2009) J Proteome Res , vol.8 , pp. 3737-3745
    • Spivak, M.1    Weston, J.2    Bottou, L.3    Kall, L.4    Noble, W.S.5
  • 66
    • 84876329019 scopus 로고    scopus 로고
    • A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies
    • Jagtap P, Goslinga J, Kooren JA, McGowan T, Wroblewski MS, et al. (2013) A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies. Proteomics 13: 1352-1357.
    • (2013) Proteomics , vol.13 , pp. 1352-1357
    • Jagtap, P.1    Goslinga, J.2    Kooren, J.A.3    McGowan, T.4    Wroblewski, M.S.5
  • 69
    • 77957221582 scopus 로고    scopus 로고
    • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics
    • Nesvizhskii AI (2010) A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 73: 2092-2123.
    • (2010) J Proteomics , vol.73 , pp. 2092-2123
    • Nesvizhskii, A.I.1
  • 70
    • 84872272080 scopus 로고    scopus 로고
    • Current algorithmic solutions for peptidebased proteomics data generation and identification
    • Hoopmann MR, Moritz RL (2013) Current algorithmic solutions for peptidebased proteomics data generation and identification. Curr Opin Biotechnol 24: 31-38.
    • (2013) Curr Opin Biotechnol , vol.24 , pp. 31-38
    • Hoopmann, M.R.1    Moritz, R.L.2
  • 71
  • 73
    • 84861964286 scopus 로고    scopus 로고
    • Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis
    • Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, et al. (2012) Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 336: 1314-1317.
    • (2012) Science , vol.336 , pp. 1314-1317
    • Iliev, I.D.1    Funari, V.A.2    Taylor, K.D.3    Nguyen, Q.4    Reyes, C.N.5
  • 74
    • 84862880706 scopus 로고    scopus 로고
    • Mucosal immunology: Don't forget our fungal friends
    • Minton K (2012) Mucosal immunology: Don't forget our fungal friends. Nat Rev Immunol 12: 476.
    • (2012) Nat Rev Immunol , vol.12 , pp. 476
    • Minton, K.1
  • 76
    • 84855533919 scopus 로고    scopus 로고
    • Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry
    • Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, et al. (2012) Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. J Proteome Res 11: 247-260.
    • (2012) J Proteome Res , vol.11 , pp. 247-260
    • Prasad, T.S.1    Harsha, H.C.2    Keerthikumar, S.3    Sekhar, N.R.4    Selvan, L.D.5


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