Prospective biomarker studies can be used to identify biomarkers predictive of disease onset. However, if serum biomarkers are measured years after their collection, the storage conditions might affect analyte concentrations. Few data exists concerning which metabolites and proteins are affected by storage at - 20 °C vs - 80 °C. Our objectives were to document analytes affected by storage of serum samples at - 20 °C vs - 80 °C, and to identify those indicative of the storage temperature. We utilized liquid chromatography tandem mass spectrometry and Luminex to quantify 300 analytes from serum samples of 16 Finnish individuals with type 1 diabetes, with split-aliquot samples stored at - 80 °C and - 20 °C for a median of 4.2 years. Results were validated in 315 Finnish and 916 Scottish individuals with type 1 diabetes, stored at - 20 °C and at - 80 °C, respectively. After quality control, we analysed 193 metabolites and proteins of which 120 were apparently unaffected and 15 clearly susceptible to storage at - 20 °C vs - 80 °C. Further, we identified serum glutamate/glutamine ratio greater than 0.20 as a biomarker of storage at - 20 °C vs - 80 °C. The results provide a catalogue of analytes unaffected and affected by storage at - 20 °C vs - 80 °C and biomarkers indicative of sub-optimal storage.