1.1.1 OrganMartinis, J., Glauser, G., Valimareanu, S., and Kessler, F. (2013). A chloroplast ABC1-like kinase regulates vitamin E metabolism in Arabidopsis. Plant Physiol. 162, 652Ð62. doi:10.1104/pp.113.218644.
lipids were extracted from 100mg of fresh tissue
1.1.3 Growth condition
Tomato plants (S. lycopersicum L.) variety M82, grown on soil under conditions referred to as control (250µmol. m-2.sec-1 of light, 16-h light/8h dark, at 20¡/18¡C, with 55% relative air humidity).
1.1.4 Experimental condition
5 to 6-week old plants were transferred to either 10/8¡C (day/night), 38/30¡C or remained in 20/18¡C as control conditions. After six days plants that were all returned to control conditions for a recovery period of 5 days.
1.1.5 Sampling and sampling date
The leaves were harvested in April in 2014.
1.1.6 Metabolism quenching method
Leaves of each sample was harvested. All the plant materials were frozen immediately in liquid nitrogen to quench the enzymatic activity.
1.2 Chemical analysis metadata
1.2.1 Sample processing and extraction
lipids were extracted from 100mg of fresh tissue and suspended in 1ml of tetrahydrofuran:methanol 50:50 (v/v). 5-10 glass beads (1 mm in diameter) were added to the mixture and homogenized for 3 min at 30 Hz in a tissue lyser. After centrifugation (3 min, 14 000 g, and 4 ¡C), the supernatant was transferred to an HPLC vial. Lipid profiles were obtained by ultra-high pressure liquid chromatography coupled with atmospheric pressure chemical ionization-quadrupole time-of-ßight mass spectrometry (UHPLC-APCI-QTOF-MS) as described in Martinis et al. (2011, 2013).
1.2.2 UHPLC-APCI-QTOF-MS conditions
Separation was performed on a reverse-phase Acquity BEH C18 column (50 _ 2.1 mm, 1.7 _m) under the following conditions: solvent A=water; solvent B=methanol; 80Ð100% B in 3 min, 100% B for 2 min, re-equilibration at 80% B for 0.5 min. The flow rate was 0.8 ml minÐ1 and the injection volume was 2.5 _l. Data were acquired using MassLynx version 4.1 (Waters), and further processed with MarkerLynx XS (Waters) to generate peak lists consisting of variables described by mass-to-charge ratio and retention time. Multivariate analysis was carried out using the statistics softwares EZinfo and Simca v.13.0.3 (Umetrics).
1.2.3 Data processing
Multivariate analysis was carried out using the statistics softwares EZinfo and Simca v.13.0.3 (Umetrics). Variables were Pareto-scaled before applying principal component analysis (PCA) and supervised partial least square discriminant analysis (PLS-DA) (Eugeni Piller et al., 2011; Martinis et al., 2011). In Pareto scaling, variables are divided by the square-root of their standard deviation as an intermediate between no scaling and dividing variables by their standard deviation alone. PLS-DA is a supervised multivariate method which takes advantage of class information. For PLS-DA models, the predictive ability and the degree of overfitting were evaluated using a leave-one-subject-out cross-validation and permutation tests with 200 random permutations. R2 and Q2 coefficient values were calculated for the original and permuted models. Identification of the variables of interest was achieved through comparison with pure standards whenever available. When standards were not available, tentative identification was performed by combining determination of elemental compositions (with accurate mass and isotopic ratios provided by QTOF-MS), fragmentation by collision induced dissociation to obtain characteristic fragments, and search in online databases such as LIPID MAPS (http://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=SetupTextOntologySearch) and PUBCHEM (https://pubchem.ncbi.nlm.nih.gov/search/search.cgi#).
Martinis, J., Kessler, F., and Glauser, G. (2011). A novel method for prenylquinone profiling in plant tissues by ultra-high pressure liquid chromatography-mass spectrometry. Plant Methods 7, 23. doi:10.1186/1746-4811-7-23.
Eugeni Piller, L., Besagni, C., Ksas, B., Rumeau, D., Brehelin, C., Glauser, G., et al. (2011). Chloroplast lipid droplet type II NAD(P)H quinone oxidoreductase is essential for prenylquinone metabolism and vitamin K1 accumulation. Proc. Natl. Acad. Sci. 108, 14354Ð14359. doi:10.1073/pnas.1104790108.
Gruszka, J., and Kruk, J. (2007). RP-LC for determination of plastochromanol, tocotrienols and tocopherols in plant oils. Chromatographia 66, 909Ð9013. doi:10.1365/s10337-007-0416-2 0009-5893/07/12.
Kruk, J. (1988). Charge-transfer complexes of plastoquinone and _-tocopherol quinone in vitro. Biophys. Chem. 30, 143Ð149. doi:10.1016/0301-4622(88)85011-7.