Resolvin D1 (RvD1) and protectin D1 (Neuroprotectin D1, PD1/NPD1) are newly identified anti-inflammatory lipid mediators biosynthesized from docosahexaenoic acid (DHA). In this report, the spectra-structure correlations and fragmentation mechanisms were studied using electrospray low-energy collision-induced dissociation tandem mass spectrometry (MS/MS) for biogenic RvD1 and PD1, as well as mono-hydroxy-DHA and related hydroperoxy-DHA. The loss of H 2 O and CO 2 in the spectra indicates the number of functional group(s). Chain-cut ions are the signature of the positions and numbers of functional groups and double bonds. The observed chain-cut ion is equivalent to a hypothetical homolytic-segment (cc, cm, mc, or mm) with addition or extraction of up to 2 protons (H). The ␣-cleavage ions are equivalent to: [cc ϩ H], with H from the hydroxyl through a -ene or ␥-ene rearrangement; [cm Ϫ 2H], with 2H from hydroxyls of PD1 through a ␥-ene rearrangement, or 1H from the hydroxyl and the other H from the ␣-carbon of mono-HDHA through an ␣-H--ene rearrangement; [mc Ϫ H], with H from hydroxyl through a -ene or ␥-ene rearrangement, or from the ␣-carbon through an ␣-H--ene rearrangement; or [mm] through charge-direct fragmentations. The -ene or ␥-ene facilitates the H shift to ␥ position and ␣-cleavage. Deuterium labeling confirmed the assignment of MS/MS ions and the fragmentation mechanisms. Based on the MS/MS spectra and fragmentation mechanisms, we identified RvD1, PD1, and mono-hydroxy-DHA products in human neutrophils and blood, trout head-kidney, and stroke-injury murine braintissue. (J Am Soc Mass Spectrom 2007, 18, 128 -144)