Extended Data Fig. 2: Identifying small molecules by stable-isotope labeling and MS/MS.

a Breakdown of metabolites grouped by unlabeled parent compound abundance. Detection limit prevents identification of certain compounds (<10⁴) at their monoisotopic m/z and of others by their labeled compounds (<10⁵), whose abundance falls below the detection limit. b Diagram depicting the first steps of the transsulfuration pathway starting with the reaction of [U-¹³C] methionine (M6) to homocysteine (M4, in two steps, not shown) and to cystathionine and labeled fraction of cystathionine (M4) from [U-¹³C] methionine in the pancreas by LC–MS and MALDI. c Breakdown of metabolites that can be detected and then verified by MS2. d Spectra of metabolites detected in MALDI by MS2. Experimentally measured (gray) and HMDB-adopted (red) spectra are shown on the positive and negative y axes, respectively. Fragment structures are provided for an example metabolite (N-acetyl aspartate). Molecular structures depict predicted (adopted from Metlin) neutral fragments and the corresponding m/z peaks refer to the [M-H]^- ions. e. Imaging mass spectrometry of unlabeled C₆H₁₂O₆ signal intensity (mixture of glucose and inositol) in murine kidney. f. LC–MS analysis showing the relative abundance of the isomers glucose and inositol in the dissected renal cortex and medulla. Scale bars: 1 mm. n = 3 for all experiments unless otherwise indicated. Data presented as mean + /- s.d.