*4.5. Data Analysis*

Metabolomics data acquired by the CE-TOFMS system were normalized and the semi-quantitative and absolute quantification data were then analyzed by PCA and PLS [34] usingMATLAB (TheMathWorks, Natick, MA, USA) and R programs [35] developed by HMT Co. Ltd. Differences between high and low IMF groups were examined by Welch's *t*-test. Significant difference was defined by *p* < 0.05.

**Supplementary Materials:** The following are available online at http://www.mdpi.com/2218-1989/10/8/322/s1, Figure S1. Principal component analysis by the metabolites detected from pig plasma samples showing the di fference in the intramuscular fat contents at the two stations. Blue and red dots indicate low and high IMF pigs, respectively. (A) The PCA performed with PC1 and PC2 for pigs from MIY station; (B) The PCA performed with PC1 and PC2 for pigs from IBR station; (C) The PCA performed with PC3 and PC4 for pigs from IBR station.

**Author Contributions:** Conceptualization, M.T. and K.I.; Methodology, M.T., C.O., K.K. (Kouen Kadowaki), K.K. (Kimiko Kohira), F.H., and K.M.; Validation, M.T., A.A., M.N. and T.O.; Formal Analysis, M.T. and A.A.; Investigation, M.T.; Resources, C.O. and K.K. (Kouen Kadowaki); Data Curation, A.A., M.N. and T.O.; Writing—Original Draft Preparation, M.T.; Writing—Review & Editing, M.T., A.A., M.N., T.O., C.O., K.K. (Kouen Kadowaki), K.K. (Kimiko Kohira), F.H., K.M., and K.I.; Visualization, M.T.; Supervision, M.T.; Project Administration, K.I.; Funding Acquisition, K.I. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was supported by a gran<sup>t</sup> from the Project of the Bio-oriented Technology Research Advancement Institution, NARO (the special scheme project on advanced research and development for next-generation technology).

**Acknowledgments:** We thank Shozo Tomonaga for his constructive comments.

**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
