A discussion of exemplary datasets was already published elsewhere by members of the consortium [7]. 3. Experimental Section 3.1. Chemicals and Reagents The L-amino acids kit (Sigma-Aldrich, Co., St. Louis, MO, USA) was used for direct infusion experiments and a commercial mix of amino acids and related compounds (Sigma-Aldrich, Co., St. Louis, MO, USA) was employed in the preparation of calibration standards. Asparagine, glutamine and homoserine were purchased separately

(Sigma-Aldrich, Co., St. Louis, MO, USA) since they are not included Inhibitors,research,lifescience,medical in the commercial mix. Stable- isotope-labeled reference compounds (L-asparagine-15-N2; L-serine,2,3,3-d3; L-glutamine-2,3,3,4,4-d5; glycine-d5; D-L-alanine-2,3,3,3-d4; proline-2,5,5-d3; methionine-methyl-d3; tryptophan-2′,4′,5′,6′,7′-d5(indole-d5);

leucine-d10; valine-d8; L-histidine (ring 2-13C); L-glutamic acid-2,4,4-d3; ornithine-3,3,4,4,5,5-d6; lysine-3,3,4,4,5,5,6,6-d8; phenyl-d5-alanine; 4-hydroxyphenyl-2,6-d2-alanine-2-d1) were used as internal PKI587 standards Inhibitors,research,lifescience,medical and were purchased from Cambridge Isotope Laboratories (Andover, MA, USA) and CDN isotopes (Pointe-Claire, Quebec, Canada). The AccQ•Tag Ultra derivatization kit (AccQ•Tag Ultra borate buffer, AccQ•Tag Ultra reagent powder, and AccQ•Tag Ultra reagent diluent) was obtained from Waters Inhibitors,research,lifescience,medical Corporation (Milford, MA, USA). AccQ•Tag Ultra eluents for UPLC-ESI-MS/MS analysis were also from Waters. Inhibitors,research,lifescience,medical Ammonium acetate was purchased from Fisher (Fair Lawn, NJ, USA); ammonium hydroxide was supplied by Sigma (St. Louis, MO, USA). LC-MS grade methanol was purchased from J.T. Baker (Phillipsburg, NJ, USA).

Ultrapure water (18.2 MΩ-cm) was obtained from a MilliQ Ultrapure water system (Millipore, Bedford, MA, USA). Ultra high purity argon and nitrogen gas for mass spectrometric analysis were purchased from Speciality Gases (Radnor, PA, USA). 3.2. Plant Material Seed stocks of Arabidopsis thaliana mutants were obtained from ABRC and propagated by the central lab of the Arabidopsis Metabolomics Consortium at Iowa State University. This paper focuses on the results obtained Inhibitors,research,lifescience,medical by targeted amino acid analysis on leaf extracts of Nature Chemical Biology 69 mutant lines selected for three metabolomic experiments (E1, E2, and E3) designed by the consortium. Six biological replicates of each mutant line were provided along with control samples (Columbia (Col-0) ecotype) for each metabolomic experiment. The list of T-DNA knock-out mutants, the rationale for their selection, plant growth conditions, and protocol for plant harvesting are published elsewhere [1,7] and also available in the project database [54]. Plant material was stored at −80 °C upon arrival. 3.3. Amino Acid Extraction from Arabidopsis Samples Amino acids were extracted from 5 mg (dry weight) of Arabidopsis leaf sample with 125 μL of 50% (v/v) methanol:water solution spiked with isotopically labeled internal standards at 4 μg/mL.