메뉴 건너뛰기




Volumn 1, Issue 3, 2016, Pages

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

Author keywords

Lipidomics; MERS CoV; Metabolomics; Multi omics analysis; Proteomics; Sample preparation

Indexed keywords


EID: 85041917042     PISSN: None     EISSN: 23795077     Source Type: Journal    
DOI: 10.1128/mSystems.00043-16     Document Type: Article
Times cited : (163)

References (49)
  • 5
    • 84871363554 scopus 로고    scopus 로고
    • A biomolecular isolation framework for eco-systems biology
    • Roume H, Muller EE, Cordes T, Renaut J, Hiller K, Wilmes P. 2013. A biomolecular isolation framework for eco-systems biology. ISME J 7:110–121. http://dx.doi.org/10.1038/ismej.2012.72.
    • (2013) ISME J , vol.7 , pp. 110-121
    • Roume, H.1    Muller, E.E.2    Cordes, T.3    Renaut, J.4    Hiller, K.5    Wilmes, P.6
  • 6
    • 84903301540 scopus 로고    scopus 로고
    • A universal protocol for the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms
    • Valledor L, Escandón M, Meijón M, Nukarinen E, Cañal MJ, Weckwerth W. 2014. A universal protocol for the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms. Plant J 79:173–180. http://dx.doi.org/10.1111/tpj.12546.
    • (2014) Plant J , vol.79 , pp. 173-180
    • Valledor, L.1    Escandón, M.2    Meijón, M.3    Nukarinen, E.4    Cañal, M.J.5    Weckwerth, W.6
  • 7
    • 0942265392 scopus 로고    scopus 로고
    • Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks
    • Weckwerth W, Wenzel K, Fiehn O. 2004. Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4:78–83. http://dx.doi.org/10.1002/pmic.200200500.
    • (2004) Proteomics , vol.4 , pp. 78-83
    • Weckwerth, W.1    Wenzel, K.2    Fiehn, O.3
  • 8
    • 84905492671 scopus 로고    scopus 로고
    • Simultaneous extraction of proteins and metabolites from cells in culture
    • Sapcariu SC, Kanashova T, Weindl D, Ghelfi J, Dittmar G, Hiller K. 2014. Simultaneous extraction of proteins and metabolites from cells in culture. Methods 1:74–80. http://dx.doi.org/10.1016/j.mex.2014.07.002.
    • (2014) Methods , vol.1 , pp. 74-80
    • Sapcariu, S.C.1    Kanashova, T.2    Weindl, D.3    Ghelfi, J.4    Dittmar, G.5    Hiller, K.6
  • 9
    • 0036182507 scopus 로고    scopus 로고
    • A comparison of cell and tissue extraction techniques using high-resolution 1H-NMR spectroscopy
    • Le Belle JE, Harris NG, Williams SR, Bhakoo KK. 2002. A comparison of cell and tissue extraction techniques using high-resolution 1H-NMR spectroscopy. NMR Biomed 15:37–44. http://dx.doi.org/10.1002/nbm.740.
    • (2002) NMR Biomed , vol.15 , pp. 37-44
    • Le Belle, J.E.1    Harris, N.G.2    Williams, S.R.3    Bhakoo, K.K.4
  • 10
    • 84869124886 scopus 로고    scopus 로고
    • Simultaneously extracting DNA, RNA, and protein using kits: Is sample quantity or quality prejudiced?
    • Mathieson W, Thomas GA. 2013. Simultaneously extracting DNA, RNA, and protein using kits: is sample quantity or quality prejudiced? Anal Biochem 433:10–18. http://dx.doi.org/10.1016/j.ab.2012.10.006.
    • (2013) Anal Biochem , vol.433 , pp. 10-18
    • Mathieson, W.1    Thomas, G.A.2
  • 11
    • 33845261493 scopus 로고
    • A rapid method of total lipid extraction and purification
    • Bligh EG, Dyer WJ. 1959. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917. http://dx.doi.org/10.1139/o59-099.
    • (1959) Can J Biochem Physiol , vol.37 , pp. 911-917
    • Bligh, E.G.1    Dyer, W.J.2
  • 13
    • 84872650023 scopus 로고    scopus 로고
    • Two strings to the systems biology bow: Co-extracting the metabolome and proteome of yeast
    • Schmidt SA, Jacob SS, Ahn SB, Rupasinghe T, Krömer JO, Khan A, Varela C. 2013. Two strings to the systems biology bow: co-extracting the metabolome and proteome of yeast. Metabolomics 9:173–188. http://dx.doi.org/10.1007/s11306-012-0437-1.
    • (2013) Metabolomics , vol.9 , pp. 173-188
    • Schmidt, S.A.1    Jacob, S.S.2    Ahn, S.B.3    Rupasinghe, T.4    Krömer, J.O.5    Khan, A.6    Varela, C.7
  • 15
    • 84929378123 scopus 로고    scopus 로고
    • Comprehensive metabolomic, Lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis
    • Pomraning KR, Wei S, Karagiosis SA, Kim YM, Dohnalkova AC, Arey BW, Bredeweg EL, Orr G, Metz TO, Baker SE. 2015. Comprehensive metabolomic, Lipidomic and microscopic profiling of Yarrowia lipolytica during lipid accumulation identifies targets for increased lipogenesis. PLoS One 10: e0123188.http://dx.doi.org/10.137 1/journal.pone.0123188.
    • (2015) PLoS One , vol.10 , pp. e0123188
    • Pomraning, K.R.1    Wei, S.2    Karagiosis, S.A.3    Kim, Y.M.4    Dohnalkova, A.C.5    Arey, B.W.6    Bredeweg, E.L.7    Orr, G.8    Metz, T.O.9    Baker, S.E.10
  • 19
    • 84899860832 scopus 로고    scopus 로고
    • Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae
    • Anderson JC, Wan Y, Kim YM, Pasa-Tolic L, Metz TO, Peck SC. 2014. Decreased abundance of type III secretion system-inducing signals in Arabidopsis mkp1 enhances resistance against Pseudomonas syringae. Proc Natl Acad Sci U S A 111:6846–6851. http://dx.doi.org/10.1073/ pnas.1403248111.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. 6846-6851
    • Anderson, J.C.1    Wan, Y.2    Kim, Y.M.3    Pasa-Tolic, L.4    Metz, T.O.5    Peck, S.C.6
  • 20
    • 0345550275 scopus 로고    scopus 로고
    • Comparison of protein precipitation methods for sample preparation prior to proteomic analysis
    • Jiang L, He L, Fountoulakis M. 2004. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis. J Chromatogr A 1023:317–320. http://dx.doi.org/10.1016/j.chroma.2003.10.029.
    • (2004) J Chromatogr A , vol.1023 , pp. 317-320
    • Jiang, L.1    He, L.2    Fountoulakis, M.3
  • 21
    • 80053418647 scopus 로고    scopus 로고
    • Assessing the need for a standardized cancer HUman biobank (caHUB): Findings from a national survey with cancer researchers
    • Massett HA, Atkinson NL, Weber D, Myles R, Ryan C, Grady M, Compton C. 2011. Assessing the need for a standardized cancer HUman biobank (caHUB): findings from a national survey with cancer researchers. J Natl Cancer Inst Monogr 2011:8–15. http://dx.doi.org/10.1093/jncimonographs/lgr007.
    • (2011) J Natl Cancer Inst Monogr , vol.2011 , pp. 8-15
    • Massett, H.A.1    Atkinson, N.L.2    Weber, D.3    Myles, R.4    Ryan, C.5    Grady, M.6    Compton, C.7
  • 22
    • 33646264529 scopus 로고    scopus 로고
    • Advances in proteomics data analysis and display using an accurate mass and time tag approach
    • Zimmer JS, Monroe ME, Qian WJ, Smith RD. 2006. Advances in proteomics data analysis and display using an accurate mass and time tag approach. Mass Spectrom Rev 25:450–482. http://dx.doi.org/10.1002/mas.20071.
    • (2006) Mass Spectrom Rev , vol.25 , pp. 450-482
    • Zimmer, J.S.1    Monroe, M.E.2    Qian, W.J.3    Smith, R.D.4
  • 23
    • 77957344363 scopus 로고    scopus 로고
    • A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin
    • Proc JL, Kuzyk MA, Hardie DB, Yang J, Smith DS, Jackson AM, Parker CE, Borchers CH. 2010. A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin. J Proteome Res 9:5422–5437. http://dx.doi.org/10.1021/pr100656u.
    • (2010) J Proteome Res , vol.9 , pp. 5422-5437
    • Proc, J.L.1    Kuzyk, M.A.2    Hardie, D.B.3    Yang, J.4    Smith, D.S.5    Jackson, A.M.6    Parker, C.E.7    Borchers, C.H.8
  • 24
    • 84885106989 scopus 로고    scopus 로고
    • Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis
    • León IR, Schwämmle V, Jensen ON, Sprenger RR. 2013. Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics 12:2992–3005. http://dx.doi.org/10.1074/mcp.M112.025585.
    • (2013) Mol Cell Proteomics , vol.12 , pp. 2992-3005
    • León, I.R.1    Schwämmle, V.2    Jensen, O.N.3    Sprenger, R.R.4
  • 25
    • 11144353532 scopus 로고    scopus 로고
    • Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry
    • Chertov O, Biragyn A, Kwak LW, Simpson JT, Boronina T, Hoang VM, Prieto DA, Conrads TP, Veenstra TD, Fisher RJ. 2004. Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry. Proteomics 4:1195–1203. http://dx.doi.org/10.1002/pmic.200300677.
    • (2004) Proteomics , vol.4 , pp. 1195-1203
    • Chertov, O.1    Biragyn, A.2    Kwak, L.W.3    Simpson, J.T.4    Boronina, T.5    Hoang, V.M.6    Prieto, D.A.7    Conrads, T.P.8    Veenstra, T.D.9    Fisher, R.J.10
  • 28
    • 84860854049 scopus 로고    scopus 로고
    • Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics
    • Shi T, Su D, Liu T, Tang K, Camp DG, II, Qian WJ, Smith RD. 2012. Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics. Proteomics 12:1074–1092. http://dx.doi.org/10.1002/pmic.201100436.
    • (2012) Proteomics , vol.12 , pp. 1074-1092
    • Shi, T.1    Su, D.2    Liu, T.3    Tang, K.4    Camp, D.G.5    Qian, W.J.6    Smith, R.D.7
  • 29
    • 26844559000 scopus 로고    scopus 로고
    • Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein
    • Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M. 2005. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 4:1265–1272. http://dx.doi.org/10.1074/mcp.M500061-MCP200.
    • (2005) Mol Cell Proteomics , vol.4 , pp. 1265-1272
    • Ishihama, Y.1    Oda, Y.2    Tabata, T.3    Sato, T.4    Nagasu, T.5    Rappsilber, J.6    Mann, M.7
  • 31
    • 84884994144 scopus 로고    scopus 로고
    • A new method to measure oxygen solubility in organic solvents through optical oxygen sensing
    • Quaranta M, Murkovic M, Klimant I. 2013. A new method to measure oxygen solubility in organic solvents through optical oxygen sensing. Analyst 138:6243–6245. http://dx.doi.org/10.1039/c3an36782g.
    • (2013) Analyst , vol.138 , pp. 6243-6245
    • Quaranta, M.1    Murkovic, M.2    Klimant, I.3
  • 32
    • 84941413167 scopus 로고    scopus 로고
    • Middle East respiratory syndrome
    • Zumla A, Hui DS, Perlman S. 2015. Middle East respiratory syndrome. Lancet 386:995–1007 http://dx.doi.org/10.1016/S0140-6736(15)60454-8.
    • (2015) Lancet , vol.386 , pp. 995-1007
    • Zumla, A.1    Hui, D.S.2    Perlman, S.3
  • 35
    • 58349105009 scopus 로고    scopus 로고
    • LRpath: A logistic regression approach for identifying enriched biological groups in gene expression data
    • Sartor MA, Leikauf GD, Medvedovic M. 2009. LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. BioInformatics 25:211–217. http://dx.doi.org/10.1093/bioinformatics/btn592.
    • (2009) BioInformatics , vol.25 , pp. 211-217
    • Sartor, M.A.1    Leikauf, G.D.2    Medvedovic, M.3
  • 36
    • 77952315185 scopus 로고    scopus 로고
    • Integration of -omics data and networks for biomedical research with vaned
    • Klukas C, Schreiber F. 2010. Integration of -omics data and networks for biomedical research with vaned. J Integr Bioinform 7:112. http://dx.doi.org/10.2390/biecoll-jib-2010-112.
    • (2010) J Integr Bioinform , vol.7 , pp. 112
    • Klukas, C.1    Schreiber, F.2
  • 37
    • 84957362388 scopus 로고    scopus 로고
    • Sphingolipids in viral infection
    • Schneider-Schaulies J, Schneider-Schaulies S. 2015. Sphingolipids in viral infection. Biol Chem 396:585–595. http://dx.doi.org/10.1515/hsz-2014-0273.
    • (2015) Biol Chem , vol.396 , pp. 585-595
    • Schneider-Schaulies, J.1    Schneider-Schaulies, S.2
  • 38
    • 0033918950 scopus 로고    scopus 로고
    • Sindbis virus entry into cells triggers apoptosis by activating sphingomyelinase, leading to the release of ceramide
    • Jan JT, Chatterjee S, Griffin DE. 2000. Sindbis virus entry into cells triggers apoptosis by activating sphingomyelinase, leading to the release of ceramide. J Virol 74:6425–6432. http://dx.doi.org/10.1128/JVI.74.14.6425-6432.2000.
    • (2000) J Virol , vol.74 , pp. 6425-6432
    • Jan, J.T.1    Chatterjee, S.2    Griffin, D.E.3
  • 39
    • 84881416314 scopus 로고    scopus 로고
    • Anti-dengue virus nonstructural protein 1 antibodies cause NO-mediated endothelial cell apoptosis via ceramide-regulated glycogen synthase kinase-3beta and NF-kappaB activation
    • Chen CL, Lin CF, Wan SW, Wei LS, Chen MC, Yeh TM, Liu HS, Anderson R, Lin YS. 2013. Anti-dengue virus nonstructural protein 1 antibodies cause NO-mediated endothelial cell apoptosis via ceramide-regulated glycogen synthase kinase-3beta and NF-kappaB activation. J Immunol 191:1744–1752. http://dx.doi.org/10.4049/jimmunol.1201976.
    • (2013) J Immunol , vol.191 , pp. 1744-1752
    • Chen, C.L.1    Lin, C.F.2    Wan, S.W.3    Wei, L.S.4    Chen, M.C.5    Yeh, T.M.6    Liu, H.S.7    Anderson, R.8    Lin, Y.S.9
  • 40
    • 84883262923 scopus 로고    scopus 로고
    • Bilateral entry and release of Middle East respiratory syndrome coronavirus induces profound apoptosis of human bronchial epithelial cells
    • Tao X, Hill TE, Morimoto C, Peters CJ, Ksiazek TG, Tseng CT. 2013. Bilateral entry and release of Middle East respiratory syndrome coronavirus induces profound apoptosis of human bronchial epithelial cells. J Virol 87:9953–9958. http://dx.doi.org/10.1128/JVI.01562-13.
    • (2013) J Virol , vol.87 , pp. 9953-9958
    • Tao, X.1    Hill, T.E.2    Morimoto, C.3    Peters, C.J.4    Ksiazek, T.G.5    Tseng, C.T.6
  • 41
    • 70449158340 scopus 로고
    • A simple method for the isolation and purification of total lipides from animal tissues
    • Folch J, Lees M, Sloane SGH. 1957. A simple method for the isolation and purification of total lipides from animal tissues. J Biol Chem 226: 497–509.
    • (1957) J Biol Chem , vol.226 , pp. 497-509
    • Folch, J.1    Lees, M.2    Sloane, S.G.H.3
  • 42
    • 34548136221 scopus 로고    scopus 로고
    • VIPER: An advanced software package to support high-throughput LC-MS peptide identification
    • Monroe ME, Tolic N, Jaitly N, Shaw JL, Adkins JN, Smith RD. 2007. VIPER: an advanced software package to support high-throughput LC-MS peptide identification. BioInformatics 23:2021–2023. http://dx.doi.org/10.1093/bioinformatics/btm281.
    • (2007) BioInformatics , vol.23 , pp. 2021-2023
    • Monroe, M.E.1    Tolic, N.2    Jaitly, N.3    Shaw, J.L.4    Adkins, J.N.5    Smith, R.D.6
  • 44
    • 66149088821 scopus 로고    scopus 로고
    • MetaboliteDetector: Comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis
    • Hiller K, Hangebrauk J, Jäger C, Spura J, Schreiber K, Schomburg D. 2009. MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal Chem 81: 3429–3439. http://dx.doi.org/10.1021/ac802689c.
    • (2009) Anal Chem , vol.81 , pp. 3429-3439
    • Hiller, K.1    Hangebrauk, J.2    Jäger, C.3    Spura, J.4    Schreiber, K.5    Schomburg, D.6
  • 46
    • 78149378686 scopus 로고    scopus 로고
    • Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data
    • Webb-Robertson BJ, McCue LA, Waters KM, Matzke MM, Jacobs JM, Metz TO, Varnum SM, Pounds JG. 2010. Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data. J Proteome Res 9:5748–5756. http://dx.doi.org/10.1021/pr1005247.
    • (2010) J Proteome Res , vol.9 , pp. 5748-5756
    • Webb-Robertson, B.J.1    McCue, L.A.2    Waters, K.M.3    Matzke, M.M.4    Jacobs, J.M.5    Metz, T.O.6    Varnum, S.M.7    Pounds, J.G.8
  • 48
    • 82955187002 scopus 로고    scopus 로고
    • A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors
    • Webb-Robertson BJ, Matzke MM, Jacobs JM, Pounds JG, Waters KM. 2011. A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors. Proteomics 11:4736 – 4741. http://dx.doi.org/10.1002/pmic.201100078.
    • (2011) Proteomics , vol.11 , pp. 4736-4741
    • Webb-Robertson, B.J.1    Matzke, M.M.2    Jacobs, J.M.3    Pounds, J.G.4    Waters, K.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.