Thirty-five out of the 38 targeted amino acids were identified and detected above their LODs in the A. thaliana leaf extracts. Figure 2 shows the amino acid profiles of two mutant stocks carrying T-DNA mutant alleles in genes of known function (GKFs) and GUFs. Quantitation was based on relative peak areas (as

response) of each compound using the calibration curves that were constructed employing the internal standard method. Asparagine (Asn), serine (Ser), Inhibitors,research,lifescience,medical glutamine (Gln), arginine (Arg), glycine (Gly), ethanolamine (MEA), aspartic acid (Asp), threonine (Thr), L-alanine (L-Ala), γ-amino-n-butyric acid (Gaba), proline (Pro), lysine (Lys), valine (Val), isoleucine (Ile) were among the most abundant amino acids in the extracts. Inhibitors,research,lifescience,medical 3-Methyl-histidine (3-Mehis), 1-methyl-histidine (1-Mehis), creatinine (Cr), cystathionine (Cysthi), cystine (Cys-S-S-cys), cysteine (Cys), and homocysteine (Hcy) were not detected (below LOD) in any of the samples studied (wild-type and mutants). Details on the statistical data processing were already published in two previous papers by the Arabidopsis Metabolomics Consortium [1,7] Inhibitors,research,lifescience,medical and will not be covered in this paper. Data quality

check performed to determine the variability in amino acid concentration between different biological replicates showed correlation coefficients between 0.61–1.00. Correlation coefficients Inhibitors,research,lifescience,medical were < 0.7 in the majority of the cases, indicating the high reliability between the

replicates obtained with our amino acid profiling platform. Figure S3 shows the data quality plot for the analysis of amino Inhibitors,research,lifescience,medical acids in the mutant SALK_021108 (AT1G52670). Data quality plots for all the mutants analyzed with our AccQ•Tag-UPLC-MS/MS platform can be found in the web portal of the consortium [54]. Figure 2 Amino acid profiles in Arabidopsis mutant stocks carrying T-DNA mutant alleles in GKF and GUF. (A) Concentration of amino acids (μmol mg−1 dry Etomidate weight) in mutant line SALK_021108 compared to its parental strain (wild-type). (B) Concentration … It is obvious that the amino acid profiling alone is not AZD0530 cell line enough to represent the metabolic effect of gene knockout in the group of T-DNA mutants stocks selected in the initial three metabolomic experiments (E1, E2 and E3) and, therefore, interpretation of the biological significance of the data is outside the scope of this manuscript. However, the combination of our AccQ•Tag-UPLC-ESI-MS/MS platform with other targeted and untargeted method gives a more holistic view of changes in the metabolome.