Water samples were collected with CTD rosette samplers (SeaBird SBE 911Plus) at two depths (deep chlorophyll maximum and bottom water) during two cruises in 2022: the RV Maria S. Merian cruise MSM107 to the western Irish shelf and the RV Endeavor cruise EN683 to the northwest Atlantic. Water was collected at one station during each cruise. Immediately after collection seawater was filtered through a 0.22 µm polyethersulfone filter and oligosaccharides were extracted with Supelclean™ ENVI-Carb™ SPE cartridges (60 mL, 10 g) from 600 mL samples. Processing blanks were also extracted on board using Sigma sea salts dissolved in MilliQ-water. Extracts were acid hydrolysed (1 M HCl, 24 h, 100°C), and the released monosaccharides were derivatised with 1-phenyl-3-methyl-5-pyrazolone (PMP) and quantified by LC-MS/MS (Xu et al., 2018, doi:10.1039/C7AN01530E). Sugar derivatives were separated on a C18 column and detected with a SCIEX qTRAP5500 mass spectrometer in multiple reaction monitoring (MRM) mode. The monosaccharide concentration file contains the calculated concentrations of monosaccharides in samples after normalisation with respect to internal standards, calibration against standard curves and division by the concentration factor. Processing blanks are referred to as having sample type of 'Artificial seawater extract' and seawater extracts as 'Seawater extract'.