During the MOSAiC expedition in the Central Arctic Ocean (CAO, 2019-2020), POM was sampled weekly to fortnightly from surface waters and the Chlorophyll a maximum layer (Chl a max) via CTD casts and from bottom sea ice of the floe via ice coring (first- and second-year ice, two layers nearest to the water-ice interface). The POM was filtered onboard (GF/F filters) and deep frozen for the subsequent analysis of a suite of lipid biomarkers, including IP25 and other highly-branched isoprenoids (HBI), fatty acids (FA) and sterols. These biomarkers can provide valuable information about the nutritional value, the taxonomic composition (e.g. diatoms vs flagellates), and the origin of the POM that represents the basis of the Central Arctic food web. This dataset comprises the results from the HBI analysis only, while the FA dataset is already published and the sterol data will be submitted shortly. The separation of the various lipid biomarkers was carried out at the University of Plymouth. After addition of internal standards for each of the 3 components, the filters were saponified with KOH. Thereafter, non-saponifiable lipids (HBI and sterols) were extracted with hexane and purified by open column chromatography (SiO2). Fatty acids were obtained by adding concentrated HCl to the saponified solution and re-extracted with hexane. The analysis of IP25 was carried out using an Agilent 7890A gas chromatograph (GC), coupled to an Agilent 5975 mass selective detector (mass spectrometry, MS), fitted with an Agilent HP-5ms column with auto-splitless injection and helium carrier gas. Identification of IP25 and other HBIs was achieved by comparison of their individual GC retention indices and mass spectra with those obtained from purified standards. IP25 was quantified by, first, integrating individual ion responses in selected-ion monitoring mode (m/z 350.3), second, normalising these to the corresponding peak area of the internal standard and, third, applying an instrumental response factor obtained from a purified standard. These IP25 quantities per filter can be normalised to the volume of filtered seawater or melted ice core water. Contributions by KS were funded by the UK's Natural Environment Research Council MOSAiC Thematic project SYM-PEL: ''Quantifying the contribution of sympagic versus pelagic diatoms to Arctic food webs and biogeochemical fluxes: application of source-specific highly branched isoprenoid biomarkers''/ (NE/S002502/1)

Calanus hyperboreus dominates the copepod biomass in the high Arctic. It forms an important intermediate trophic level in the Central Arctic food web, grazing on algae and protists and serving as prey for a large range of other zooplankton, fish and seabirds. Their unique lipids (20:1, 22:1 fatty acids and fatty alcohols) can be traced within the Arctic megafauna from seals to whales and polar bears, as these energy-rich lipids are crucial body reserves for the dark season. During the MOSAiC expedition in the Central Arctic Ocean (CAO, 2019-2020), C. hyperboreus adult females (AF) and subadult copepodites stages (CV) were sampled weekly to fortnightly. A range of nets were used to sample either horizontally underneath the sea ice or vertically from maximum 2000 m through the water column. Onboard, ~10 AF and ~20 CV of C. hyperboreus were sorted from each catch, photographed, rinsed with freshwater to remove salt and frozen at -80C for subsequent analysis of their total dry mass (DM), lipid content and a suite of trophic markers, including bulk stable isotopes (BSI), phytosterols (PS), total fatty acids (TFA), total fatty alcohols (TFAlc), and highly-branched isoprenoids (HBI). During the time of their seasonal descent at the end of summer, vertical sampling of C. hyperboreus was intensified and additional parameters were analysed, e.g. the FA and FAlc composition of their storage lipids (neutral lipids, NLFA, NLFAlc) and membrane lipids (polar lipids, PLFA, PLFAlc), the carbon isotopic composition of key FA and FAlc (CSIA-FA; CSIA-FAlc), and the tissue density. By combining this array of trophic markers, valuable information about the body conditions and feeding history of these copepods can be linked to their life cycle and vertical distribution. The initial separation of the various trophic markers was carried out at the University of Plymouth. After estimating the total DM, subsamples for BSI were sent to the Littoral, Environment and Societies Joint Research Unit stable isotope facility (CNRS - University of La Rochelle, France) for analysis. Three internal standards were added to the samples used for lipid analysis to quantify the TFA, TFAlc, PS and HBI content. As a first step, the total lipid content of the animals was extracted in dichloromethane : methanol. The lipid samples were split into two equal subsamples, one was sent to the Alfred-Wegener-Institute (AWI) in Bremerhaven/Germany for FA and FAlc analyses and the second was used for PS and HBI analyses in Plymouth. This dataset is linked to a manuscript that compares the trophic marker composition of C. hyperboreus from the surface vs. deep ocean to understand drivers, benefits, and risks of their seasonal migration in the CAO. The manuscript focusses mainly on the copepod descent in late summer and the changes in body conditions and trophic marker composition over the winter months. Contributions by KS were funded by the UK's Natural Environment Research Council MOSAiC Thematic project SYM-PEL: "Quantifying the contribution of sympagic versus pelagic diatoms to Arctic food webs and biogeochemical fluxes: application of source-specific highly branched isoprenoid biomarkers" (NE/S002502/1). CJA, RGC, CEG, KMS and RJ were funded by the US National Science Foundation Office of Polar Programs (OPP-1824447 and OPP-1824414).

During the MOSAiC expedition in the Central Arctic Ocean (CAO, 2019-2020), POM was sampled weekly to fortnightly from surface waters and the Chlorophyll a maximum layer (Chl a max) via CTD casts and from bottom sea ice of the floe via ice coring (first- and second-year ice, two layers nearest to the water-ice interface). The POM was filtered onboard (GF/F filters) and deep frozen for the subsequent analysis of a suite of lipid biomarkers, including fatty acids (FA), FA-compound-specific stable isotopes (FA-CSIA), sterols, and highly-branched isoprenoids (HBI). These biomarkers can provide valuable information about the nutritional value, the taxonomic composition (e.g. diatoms vs flagellates), and the origin of the POM that represents the basis of the Central Arctic food web. This dataset comprises the results from the FA analysis only, those from other biomarkers will be submitted in due cause. The separation of the various lipid biomarkers was carried out at the University of Plymouth. After addition of internal standards for each of the 3 components, the filters were saponified with KOH. Thereafter, non-saponifiable lipids (HBI and sterols) were extracted with hexane and purified by open column chromatography (SiO2). Fatty acids were obtained by adding concentrated HCl to the saponified solution and re-extracted with hexane. Further steps of the FA analysis were carried out at the Alfred-Wegener-Institute (AWI) in Bremerhaven. Here samples were converted into fatty acid methyl esters (FAME) and analysed using an Agilent 6890N gas chromatograph. The Clarity chromatography software system (DataApex, Czech Republic) was used for chromatogram data evaluation. FAME were quantified via the internal standard, Tricosanoic acid methyl ester (23:0) (Supelco, Germany) to provide the total amount of FA (TFA) per filter. These TFA quantities per filter can be normalised to the volume of filtered seawater or melted ice core water. Additionally, we provide the mass percentage composition of the TFA, considering 48 individual FA. The FA are presented in shorthand notation, i.e., A:B(n-x), where: A indicates the number of carbon atoms in the straight fatty acid chain, B represents the number of double bonds present, n represents the terminal methyl group and x denotes the position of the first double bond from the terminal end. The biochemical nomenclature of the fatty acids is provided. The dataset is linked to a manuscript that compares pattern seen in sea ice- and water column POM in the CAO with previously published data from Arctic shelf regions. This manuscript focusses mainly on two key long-chain omega-3 FA (eicosapentaenoic acid and docosahexaenoic acid) that are considered essential for the nutrition of higher trophic levels, including humans, and their production to decline with global temperature rise. Contributions by KS were funded by the UK's Natural Environment Research Council MOSAiC Thematic project SYM-PEL: "Quantifying the contribution of sympagic versus pelagic diatoms to Arctic food webs and biogeochemical fluxes: application of source-specific highly branched isoprenoid biomarkers" (NE/S002502/1).

At the basis of the marine Arctic food web, there are several carbon sources including ice-associated (sympagic) algae that live primarily in sea ice, melt ponds or underneath sea ice; pelagic algae that live primarily in open waters; terrestrial detritus that got incorporated into sea ice forming on the Siberian Shelf and being transported with the transpolar drift across the Central Arctic Ocean (CAO); and detritus that derives with currents from the Atlantic ocean. Copepods and amphipods are diverse and often biomass-dominant zooplankton groups in the CAO that include taxa specialised in feeding on algae and small heterotrophs, on sinking detritus or other zooplankton. Gelatinous (cnidaria, appendicularia) and semi-gelatinous (chaetognaths) taxa, ostracods, pteropods, euphausiids and pelagic decapods are other important zooplankton groups in the CAO that likewise feed on a range of food sources. With the loss of Arctic sea ice, the relative importance of ice-associated carbon in the Arctic food web became a central research topic, and multiple trophic marker approaches have been developed to distinguish between pelagic and sympagic carbon transfer to higher trophic levels. During the MOSAiC expedition in the CAO (2019-2020), zooplankton was sampled weekly to fortnightly. A range of nets were used to sample either horizontally underneath the sea ice or vertically from a maximum depth of 2000 m to the surface. Onboard, abundant zooplankton taxa were sorted from each catch, photographed, rinsed with freshwater to remove salt and frozen at -80 degrees Celsius for subsequent analysis of their total dry mass (DM), lipid content, lipid classes and a suite of trophic markers, including bulk stable isotopes (BSI), phytosterols (PS), total fatty acids (TFA), total fatty alcohols (TFAlc), highly-branched isoprenoids (HBI) and the carbon isotopic composition of key FA and FAlc (CSIA-FA; CSIA-FAlc). We had ~10 target species that were sampled in all seasons (the copepods C. hyperboreus, C. glacialis, Metridia longa, the ice amphipods Apherusa glacialis and Eusirus spp., the pelagic amphipods Themisto abyssorum and T. libellula, the euphausiid Thysanoessa spp., chaetognaths and the shrimp H. glacialis). Further zooplankton taxa were collected when available in the net catches and time permitted. Additionally, Polar cod was collected in early and late summer. The initial separation of the various trophic markers was carried out at the University of Plymouth. After estimating the total DM, subsamples for BSI were sent to the Littoral, Environment and Societies Joint Research Unit stable isotope facility (CNRS - University of La Rochelle, France) for analysis. Three internal standards were added to the samples used for lipid analysis to quantify the TFA, TFAlc, PS and HBI content. As a first step, the total lipid content of the animals was extracted in dichloromethane : methanol. The lipid samples were split into two equal subsamples, one was sent to the Alfred-Wegener-Institute (AWI) in Bremerhaven/Germany for FA and FAlc analyses and the second was used for PS and HBI analyses in Plymouth. This dataset is linked to a manuscript that assesses trophic relationships in the CAO to understand the carbon fluxes in the current Arctic food web and to predict potential changes in a future ice-free Arctic. Contributions by KS were funded by the UK's Natural Environment Research Council MOSAiC Thematic project SYM-PEL: "Quantifying the contribution of sympagic versus pelagic diatoms to Arctic food webs and biogeochemical fluxes: application of source-specific highly branched isoprenoid biomarkers"/ (NE/S002502/1). CJA, RGC, CEG, KMS and RJ were funded by the US National Science Foundation Office of Polar Programs (OPP-1824447 and OPP-1824414).