Workflow of our GC-MS based untargeted metabolomic and targeted analyses for biomarker discovery.

<p>The number of candidate metabolites analyzed at specific steps is shown in parenthesis.</p

Example of a retrieved EIC for valine.

<p>The inset in the top left shows the expected ratios for the fragments based on the library to guide the visual inspection. The doted vertical lines show the expected and estimated elution time of the analyte. Although, the background signal of 73 from other compounds is reflected in the apex score, its impact on the AUC is diminished by baseline correction.</p

List of nine analytes confirmed by targeted analysis with their expected retention time and molecular weights for quantifier (M1) and qualifier fragments (M2-M3).

<p>* Number of TMS in Fiehn library</p><p>Fragment with a molecular weight of 73 was also monitored by default for all the analytes.</p

Characteristics of the study cohort.

<p>Characteristics of the study cohort.</p

Metabolites with significant changes in their levels in HCC vs. cirrhosis based on targeted analysis of plasma by GC-SIM-MS.

<p>The metabolites in the top two panels show increasing trend with the progression of HCC. The metabolites in the bottom panel are down-regulated in HCC vs. cirrhosis. While lactic acid and citric acid show decreasing trend with the progression of HCC, sorbose is down-regulated overall in HCC vs. cirrhosis.</p

Pathway and network analysis of 24 metabolites recognized by IPA from the candidates discovered by GC-MS and LC-MS based analyses.

<p>A: top 10 canonical pathways based on 24 metabolites. B: network involving 13 out of the 24 metabolites (up-regulated in HCC vs. cirrhosis marked in red, down-regulated in HCC vs. cirrhosis marked in green).</p

Evaluation of the metabolites from targeted analysis using PLS-DA and OPLS-DA.

<p>A: Score plot obtained by PLS-DA with HCC cases labeled by red triangles and patients with liver cirrhosis by blue dots. Stage II & III HCC cases are labeled with solid triangles. B: Loading plot from PLS-DA. C: S-plot obtained by OPLS-DA. The nine metabolites previously selected by univariate analysis are highlighted in B and C.</p