D4 cholic acid

Samples were prepared from control and infected 5-week-old plants^{47 (link)}. 20 mg of grinded samples were mixed with 1 mL extraction buffer (20/20/60 v/v/v chloroform:water:methanol) including internal standards for GC–MS and LC–MS. LC–MS internal standards were: 13C9-phenylalanine, 13C3-caffeine, D4-cholic acid, D8-arachidonic acid and 13C9-caffeic acid (Sigma, St. Louis, MO, USA). GC–MS internal standards were: L-proline-13C5, alpha-ketoglutarate-13C4, myristic acid-13C3, cholesterol-D7 (Cambridge Isotope Laboratories, Inc., Andover, MA, USA) and succinic acid-D4, salicylic acid-D6, L-glutamic acid-13C5,15N, putrescine-D4, hexadecenoic acid-13C4, D-glucose-13C6, D-sucrose-13C12 from Sigma. The samples were bead-beated and centrifuged as described^{27 (link)}. Most of the supernatants, 200 µL for LC–MS analysis and 50 µL for GC–MS analysis, were transferred to micro vials, evaporated to dryness and stored at − 80 °C until analysis. Small aliquots of the remaining supernatants were pooled and used as quality control (QC) samples. MSMS analysis (LC–MS) was run on the QC samples for identification purposes. The samples were analyzed in batches according to a randomized run order on both GC–MS and LC–MS.

The AbsoluteIDQ^® p180 Kit was purchased from Biocrates Life Sciences AG, Innsbruck, Austria. All chemical standards of lipids were purchased from Aldrich-Fluka-Sigma S.r.l. (Milan, Italy). Labeled internal standards: D3-octanoyl L-carnitineHCl, D3-hexadecanoyl L-carnitineHCl, D3-acetyl L-carnitineHCl, D3-L-carnitine HCl, D3-eicosanoic acid, D3-octadecanoic acid (D3-stearic acid) and D3-tetradecanoic acid (D3-myristic acid) were from CDN Isotope (Quebec, Canada); D7-cholesterol, D4-cholic acid, D4-chenodeoxycholic acid, D4-glycoursodeoxycholic acid, D4-glycocholic acid, D5-taurocholic acid, D5-taurodeoxycholic acid, D4-lithocholic acid were from Sigma–Aldrich (Sigma–Aldrich, Milan, Italy). All chemicals had a purity grade greater than 90% and were used without further purification. Acetonitrile (ACN), 2-propanol (IPA), methanol (CH3OH), chloroform (CHCl3) and triethylamine (TEA) were purchased from Sigma–Aldrich (Sigma–Aldrich, Milan, Italy). All these solvents were of LC-MS grade, water was MilliQ (Millipore, Vimodrone, Milan, Italy). Formic acid (HCOOH) and ammonium formate (NH4COOH) additive for LC–MS were from FLUKA (Sigma–Aldrich, Milan, Italy).