Bruggeman FJ, Westerhoff HV. The nature of systems biology. Trends Microbiol. 2007;15(1):45–50.
Article
CAS
PubMed
Google Scholar
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Vos RCH, Moco S, Lommen A, Keurentjes JJB, Bino RJ, Hall RD. Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat Protoc. 2007;2(4):778–91.
Article
CAS
PubMed
Google Scholar
Krueger S, Steinhauser D, Willmitzer L, Giavalisco P. High-resolution plant metabolomics: from mass spectral features to metabolites and from whole-cell analysis to subcellular metabolite distributions. Plant J. 2012;70(1):39–50.
Article
CAS
Google Scholar
Blanksby SJ, Mitchell TW. Advances in mass spectrometry for lipidomics. Annu Rev Anal Chem. 2010;3:433–65.
Article
CAS
Google Scholar
Wenk MR. The emerging field of lipidomics. Nat Rev Drug Discov. 2005;4(7):594–610.
Article
CAS
PubMed
Google Scholar
Cox J, Mann M. Quantitative, high-resolution proteomics for data-driven systems biology. Annu Rev Biochem. 2011;80:273–99.
Article
CAS
PubMed
Google Scholar
Sabido E, Selevsek N, Aebersold R. Mass spectrometry-based proteomics for systems biology. Curr Opin Biotech. 2012;23(4):591–7.
Article
CAS
PubMed
Google Scholar
Abu Bakar MH, Sarmidi MR, Cheng KK, Ali Khan A, Suan CL, Zaman Huri H, Yaakob H. Metabolomics—the complementary field in systems biology: a review on obesity and type 2 diabetes. Mol BioSyst. 2015;11(7):1742–74.
Article
CAS
PubMed
Google Scholar
Toyo’oka T. Determination methods for biologically active compounds by ultra-performance liquid chromatography coupled with mass spectrometry: application to the analyses of pharmaceuticals, foods, plants, environments, metabonomics, and metabolomics. J Chromatogr Sci. 2008;46(3):233–47.
Article
PubMed
Google Scholar
Rabinowitz JD, Silhavy TJ. Systems biology: metabolite turns master regulator. Nature. 2013;500(7462):283–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dunn WB, Winder CL. Sample preparation related to the intracellular metabolome of yeast: methods for quenching, extraction, and metabolite quantitation. Methods Enzymol. 2011;500(500):277–97.
Article
CAS
PubMed
Google Scholar
Zhang AH, Sun H, Wang P, Han Y, Wang XJ. Modern analytical techniques in metabolomics analysis. Analyst. 2012;137(2):293–300.
Article
CAS
PubMed
Google Scholar
Anwar MA, Vorkas PA, Li JV, Shalhoub J, Want EJ, Davies AH, Holmes E. Optimization of metabolite extraction of human vein tissue for ultra performance liquid chromatography-mass spectrometry and nuclear magnetic resonance-based untargeted metabolic profiling. Analyst. 2015;140(22):7586–97.
Article
CAS
PubMed
Google Scholar
Sellick CA, Knight D, Croxford AS, Maqsood AR, Stephens GM, Goodacre R, Dickson AJ. Evaluation of extraction processes for intracellular metabolite profiling of mammalian cells: matching extraction approaches to cell type and metabolite targets. Metabolomics. 2010;6(3):427–38.
Article
CAS
Google Scholar
Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol. 1959;37(8):911–7.
Article
CAS
PubMed
Google Scholar
Folch J, Lees M, Stanley GHS. A simple method for the isolation and purification of total lipides from animal tissues. J Biol Chem. 1957;226(1):497–509.
CAS
PubMed
Google Scholar
Fiehn O, Kopka J, Dormann P, Altmann T, Trethewey RN, Willmitzer L. Metabolite profiling for plant functional genomics. Nat Biotechnol. 2000;18(11):1157–61.
Article
CAS
PubMed
Google Scholar
Weckwerth W, Wenzel K, Fiehn O. Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics. 2004;4(1):78–83.
Article
CAS
PubMed
Google Scholar
Fiehn O, Kopka J, Trethewey RN, Willmitzer L. Identification of uncommon plant metabolites based on calculation of elemental compositions using gas chromatography and quadrupole mass spectrometry. Anal Chem. 2000;72(15):3573–80.
Article
CAS
PubMed
Google Scholar
Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie AR. Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat Protoc. 2006;1(1):387–96.
Article
CAS
PubMed
Google Scholar
Valledor L, Escandon M, Meijon M, Nukarinen E, Canal MJ, Weckwerth W. A universal protocol for the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms. Plant J. 2014;79(1):173–80.
Article
CAS
PubMed
Google Scholar
Giavalisco P, Li Y, Matthes A, Eckhardt A, Hubberten HM, Hesse H, Segu S, Hummel J, Kohl K, Willmitzer L. Elemental formula annotation of polar and lipophilic metabolites using (13) C, (15) N and (34) S isotope labelling, in combination with high-resolution mass spectrometry. Plant J. 2011;68(2):364–76.
Article
CAS
PubMed
Google Scholar
Thomann WR, Hill GB. Modified extraction procedure for gas-liquid chromatography applied to the identification of anaerobic bacteria. J Clin Microbiol. 1986;23(2):392–4.
CAS
PubMed
PubMed Central
Google Scholar
Kuyukina MS, Ivshina IB, Philp JC, Christofi N, Dunbar SA, Ritchkova MI. Recovery of Rhodococcus biosurfactants using methyl tertiary-butyl ether extraction. J Microbiol Methods. 2001;46(2):149–56.
Article
CAS
PubMed
Google Scholar
Matyash V, Liebisch G, Kurzchalia TV, Shevchenko A, Schwudke D. Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J Lipid Res. 2008;49(5):1137–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hummel J, Segu S, Li Y, Irgang S, Jueppner J, Giavalisco P. Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. Front Plant Sci. 2011;2:54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arnon DI. Copper enzymes in isolated chloroplasts: polyphenoloxidase in beta-vulgaris. Plant Physiol. 1949;24(1):1–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ritchie RJ. Consistent sets of spectrophotometric chlorophyll equations for acetone, methanol and ethanol solvents. Photosynth Res. 2006;89(1):27–41.
Article
CAS
PubMed
Google Scholar
Porra RJ, Thompson WA, Kriedemann PE. Determination of accurate extinction coefficients and simultaneous-equations for assaying chlorophyll-a and chlorophyll-B extracted with 4 different solvents: verification of the concentration of chlorophyll standards by atomic-absorption spectroscopy. Biochim Biophys Acta. 1989;975(3):384–94.
Article
CAS
Google Scholar
Fraser PD, Enfissi EMA, Goodfellow M, Eguchi T, Bramley PM. Metabolite profiling of plant carotenoids using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Plant J. 2007;49(3):552–64.
Article
CAS
PubMed
Google Scholar
Caldana C, Li Y, Leisse A, Zhang Y, Bartholomaeus L, Fernie AR, Willmitzer L, Giavalisco P. Systemic analysis of inducible target of rapamycin mutants reveal a general metabolic switch controlling growth in Arabidopsis thaliana. Plant J. 2013;73(6):897–909.
Article
CAS
PubMed
Google Scholar
Cuadros-Inostroza A, Caldana C, Redestig H, Kusano M, Lisec J, Pena-Cortes H, Willmitzer L, Hannah MA. TargetSearch–a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics. 2009;10:428.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976;72:248–54.
Article
CAS
PubMed
Google Scholar
Rappsilber J, Mann M, Ishihama Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc. 2007;2(8):1896–906.
Article
CAS
PubMed
Google Scholar
Smith AM, Zeeman SC. Quantification of starch in plant tissues. Nat Protoc. 2006;1(3):1342–5.
Article
CAS
PubMed
Google Scholar
Hostettler C, Kolling K, Santelia D, Streb S, Kotting O, Zeeman SC. Analysis of starch metabolism in chloroplasts. Methods Mol Biol. 2011;775:387–410.
Article
CAS
PubMed
Google Scholar
Pettolino FA, Walsh C, Fincher GB, Bacic A. Determining the polysaccharide composition of plant cell walls. Nat Protoc. 2012;7(9):1590–607.
Article
CAS
PubMed
Google Scholar
Foster CE, Martin TM, Pauly M. Comprehensive compositional analysis of plant cell walls (Lignocellulosic biomass) part II: carbohydrates. J Vis Exp. 2010;(37):1837. doi:10.3791/1837.
Updegraff DM. Semimicro determination of cellulose in biological materials. Anal Biochem. 1969;32(3):420–4.
Article
CAS
PubMed
Google Scholar
Bonawitz ND, Kim JI, Tobimatsu Y, Ciesielski PN, Anderson NA, Ximenes E, Maeda J, Ralph J, Donohoe BS, Ladisch M, et al. Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant. Nature. 2014;509(7500):376–80.
Article
CAS
PubMed
Google Scholar
Bruce RJ, West CA. Elicitation of lignin biosynthesis and isoperoxidase activity by pectic fragments in suspension cultures of castor bean. Plant Physiol. 1989;91(3):889–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson AR, Mansfield SD. Rapid analysis of poplar lignin monomer composition by a streamlined thioacidolysis procedure and near-infrared reflectance-based prediction modeling. Plant J. 2009;58(4):706–14. doi:10.1111/j.1365-313X.2009.03808.x.
Article
CAS
PubMed
Google Scholar
Foster CE, Martin TM, Pauly M. Comprehensive compositional analysis of plant cell walls (Lignocellulosic biomass) part I: lignin. J Vis Exp. 2010(37):e1745. doi:10.3791/1745.
Milkowski C, Strack D. Sinapate esters in brassicaceous plants: biochemistry, molecular biology, evolution and metabolic engineering. Planta. 2010;232(1):19–35.
Article
CAS
PubMed
Google Scholar
Halkier BA, Gershenzon J. Biology and biochemistry of glucosinolates. Annu Rev Plant Biol. 2006;57:303–33.
Article
CAS
PubMed
Google Scholar
Williams CA, Grayer RJ. Anthocyanins and other flavonoids. Nat Prod Rep. 2004;21(4):539–73.
Article
CAS
PubMed
Google Scholar
Hauck OK, Scharnberg J, Escobar NM, Wanner G, Giavalisco P, Witte CP. Uric acid accumulation in an Arabidopsis urate oxidase mutant impairs seedling establishment by blocking peroxisome maintenance. Plant Cell. 2014;26(7):3090–100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Avin-Wittenberg T, Bajdzienko K, Wittenberg G, Alseekh S, Tohge T, Bock R, Giavalisco P, Fernie AR. Global analysis of the role of autophagy in cellular metabolism and energy homeostasis in Arabidopsis seedlings under carbon starvation. Plant Cell. 2015;27(2):306–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Watanabe M, Balazadeh S, Tohge T, Erban A, Giavalisco P, Kopka J, Mueller-Roeber B, Fernie AR, Hoefgen R. Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in Arabidopsis. Plant Physiol. 2013;162(3):1290–310.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lambers H, Cawthray GR, Giavalisco P, Kuo J, Laliberte E, Pearse SJ, Scheible WR, Stitt M, Teste F, Turner BL. Proteaceae from severely phosphorus-impoverished soils extensively replace phospholipids with galactolipids and sulfolipids during leaf development to achieve a high photosynthetic phosphorus-use-efficiency. New Phytol. 2012;196(4):1098–108.
Article
CAS
PubMed
Google Scholar
Degenkolbe T, Giavalisco P, Zuther E, Seiwert B, Hincha DK, Willmitzer L. Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana. Plant J 2012.
Bromke MA, Hochmuth A, Tohge T, Fernie AR, Giavalisco P, Burgos A, Willmitzer L, Brotman Y. Liquid chromatography high-resolution mass spectrometry for fatty acid profiling. Plant J. 2015;81(3):529–36.
Article
CAS
PubMed
Google Scholar
Li N, Gugel IL, Giavalisco P, Zeisler V, Schreiber L, Soll J, Philippar K. FAX1, a novel membrane protein mediating plastid fatty acid export. PLoS Biol. 2015;13(2):e1002053.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hemme D, Veyel D, Muhlhaus T, Sommer F, Juppner J, Unger AK, Sandmann M, Fehrle I, Schonfelder S, Steup M, et al. Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii. Plant Cell. 2014;26(11):4270–97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sharma DK, Gautam K, Jueppner J, Giavalisco P, Rihko-Struckmann L, Pareek A, Sundmacher K. UPLC-MS analysis of Chlamydomonas reinhardtii and Scenedesmus obliquus lipid extracts and their possible metabolic roles. J Appl Phycol. 2015;27(3):1149–59.
Article
CAS
Google Scholar
Delgado R, Munoz Y, Pena-Cortes H, Giavalisco P, Bacigalupo J. Diacylglycerol activates the light-dependent channel TRP in the photosensitive microvilli of Drosophila melanogaster photoreceptors. J Neurosci. 2014;34(19):6679–86.
Article
CAS
PubMed
Google Scholar
Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Paabo S, Sherwood CC, Hof PR, et al. Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues. Neuron. 2015;85(4):695–702.
Article
CAS
PubMed
Google Scholar
Khrameeva EE, Bozek K, He L, Yan Z, Jiang X, Wei Y, Tang K, Gelfand MS, Prufer K, Kelso J, et al. Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nat Commun. 2014;5:3584.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Paabo S, Pieszek R, Sherwood CC, et al. Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biol. 2014;12(5):e1001871.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bromke MA, Giavalisco P, Willmitzer L, Hesse H. Metabolic analysis of adaptation to short-term changes in culture conditions of the marine diatom Thalassiosira pseudonana. PLoS ONE. 2013;8(6):e67340.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tohge T, Ramos MS, Nunes-Nesi A, Mutwil M, Giavalisco P, Steinhauser D, Schellenberg M, Willmitzer L, Persson S, Martinoia E, et al. Toward the storage metabolome: profiling the barley vacuole. Plant Physiol. 2011;157(3):1469–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
Osorio S, Bombarely A, Giavalisco P, Usadel B, Stephens C, Araguez I, Medina-Escobar N, Botella MA, Fernie AR, Valpuesta V. Demethylation of oligogalacturonides by FaPE1 in the fruits of the wild strawberry Fragaria vesca triggers metabolic and transcriptional changes associated with defence and development of the fruit. J Exp Bot. 2011;62(8):2855–73.
Article
CAS
PubMed
Google Scholar
Vallarino JG, Osorio S, Bombarely A, Casanal A, Cruz-Rus E, Sanchez-Sevilla JF, Amaya I, Giavalisco P, Fernie AR, Botella MA, et al. Central role of FaGAMYB in the transition of the strawberry receptacle from development to ripening. New Phytol. 2015;208(2):482–96.
Article
CAS
PubMed
Google Scholar
Lisec J, Romisch-Margl L, Nikoloski Z, Piepho HP, Giavalisco P, Selbig J, Gierl A, Willmitzer L. Corn hybrids display lower metabolite variability and complex metabolite inheritance patterns. Plant J. 2011;68(2):326–36.
Article
CAS
PubMed
Google Scholar
Kleessen S, Irgang S, Klie S, Giavalisco P, Nikoloski Z. Integration of transcriptomics and metabolomics data specifies the metabolic response of Chlamydomonas to rapamycin treatment. Plant J. 2015;81(5):822–35.
Article
CAS
PubMed
Google Scholar
Markham JE, Jaworski JG. Rapid measurement of sphingolipids from Arabidopsis thaliana by reversed-phase high-performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. Rapid Commun Mass Sp. 2007;21(7):1304–14.
Article
CAS
Google Scholar
Markham JE, Li J, Cahoon EB, Jaworski JG. Separation and identification of major plant sphingolipid classes from leaves. J Biol Chem. 2006;281(32):22684–94.
Article
CAS
PubMed
Google Scholar
Kierszniowska S, Seiwert B, Schulze WX. Definition of Arabidopsis sterol-rich membrane microdomains by differential treatment with methyl-beta-cyclodextrin and quantitative proteomics. Mol Cell Proteomics. 2009;8(4):612–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wewer V, Dombrink I, vom Dorp K, Dormann P. Quantification of sterol lipids in plants by quadrupole time-of-flight mass spectrometry. J Lipid Res. 2011;52(5):1039–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saito K, Matsuda F. Metabolomics for functional genomics, systems biology, and biotechnology. Annu Rev Plant Biol. 2010;61:463–89.
Article
CAS
PubMed
Google Scholar
Wisniewski JR, Zougman A, Nagaraj N, Mann M. Universal sample preparation method for proteome analysis. Nat Methods. 2009;6(5):U359–60.
Article
CAS
Google Scholar
Giavalisco P, Nordhoff E, Kreitler T, Kloppel KD, Lehrach H, Klose J, Gobom J. Proteome analysis of Arabidopsis thaliana by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation-time of flight mass spectrometry. Proteomics. 2005;5(7):1902–13.
Article
CAS
PubMed
Google Scholar
Palmisano G, Lendal SE, Engholm-Keller K, Leth-Larsen R, Parker BL, Larsen MR. Selective enrichment of sialic acid-containing glycopeptides using titanium dioxide chromatography with analysis by HILIC and mass spectrometry. Nat Protoc. 2010;5(12):1974–82.
Article
CAS
PubMed
Google Scholar
Thingholm TE, Jorgensen TJ, Jensen ON, Larsen MR. Highly selective enrichment of phosphorylated peptides using titanium dioxide. Nat Protoc. 2006;1(4):1929–35.
Article
CAS
PubMed
Google Scholar
Nebrich G, Herrmann M, Hartl D, Diedrich M, Kreitler T, Wierling C, Klose J, Giavalisco P, Zabel C, Mao L. PROTEOMER: a workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics. Proteomics. 2009;9(7):1795–808.
Article
CAS
PubMed
Google Scholar