Atherosclerosis, dyslipidemia and hypertension are comorbid diseases often found in combination. Among different pharmacological approaches the employment of natural multifunctional peptides is an attractive option as side therapy. Mass spectrometry-based metabolomics provide valuable information on metabolic changes and can be useful to elucidate peptide pharmacodynamics. In this this work we performed a preliminary investigation on the potential effect of a recently characterized Spirulina platensis peptide named SP6 (GIVAGDVTPI) on the modulation of metabolism in a high fat diet ApoE-/- mice atherosclerotic model. A direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FT-ICR-MS) approach was used to elucidate polar and non-polar metabolites extracted by mice plasma following four weeks SP6 treatment. The method delivered fast analysis time, repeatability, high mass accuracy and resolution for unambiguous molecular formula assignment. Multivariate statistical analysis (PLS-DA) highlighted a clear class separation, revealing the alteration of numerous metabolites levels belonging to different classes. In particular sphingolipids, glycerophospholipids, TCA cycle intermediates, and amino acids, which are key players in the atherosclerotic process and progression, were upregulated in saline alone HFD ApoE-/- group, while were sensibly decreased after treatment with SP6 peptide. These results could open the way to further, large-scale, investigation of SP6 peptide effects in the regulation of atherosclerotic disease development and progression, and show the potential of DI-FT-ICR as fast analytical tool to take snaphshots of metabolic changes before moving to targeted MS-based approaches.