| Summary: | Rationale The efficiency of selected ion monitoring (SIM) and selected reaction monitoring (SRM) analyses for the quantification of three mono‐, di‐ and tri‐unsaturated highly branched isoprenoid (HBI) alkenes (IP 25 , IPSO 25 and HBI III, respectively), often used as proxies for the occurrence of Arctic and Antarctic sea ice or the adjacent open waters, was compared. Methods Gas chromatography (GC)–mass spectrometry (MS)/SIM and GC/MS/MS/SRM analyses were carried out on dilute solutions made from purified standards of these three HBIs, and then on hydrocarbon fractions of several sediment and sea ice sample extracts. More efficient and specific SRM transitions were selected after collision‐induced dissociation of each precursor ion at different collision energies. Results SRM analysis avoided any overestimation of IP 25 resulting from the contribution of the coeluting 13 C mass isotopomer of IPSO 25 (M + ˙ + 2) to the SIM target ion. In contrast, SRM analysis is less reliable for IPSO 25 quantification in cases where several regio‐isomers are present, likely due to intense double bond migrations following electron impact. In the case of HBI III, SRM analysis constitutes a potentially suitable alternative to SIM analysis, especially in terms of improving limit of detection. Conclusions Despite the intense migrations of HBI double bonds under electron ionization, the selected SRM transitions should be more suitable than SIM target ions for IP 25 and HBI III quantification in complex hydrocarbon fractions of natural samples. However, the advantage is less evident for IPSO 25 due to the presence of numerous regio‐isomers.
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